MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'Protein and Peptide Letters' source. Tue, 24 Jan 2012 14:11:45 +0100 http://www.medworm.com/index.php?rid=5544508&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22185497%26dopt%3DAbstract Authors: Esmaielbeiki1 R, Naughton DP, Nebel JC Abstract Human antimicrobial peptides (AMPs), including defensins, have come under intense scrutiny owing to their key multiple roles as antimicrobial agents. Not only do they display direct action on microbes, but also recently they have shown to interact with the immune system to increase antimicrobial activity. Unfortunately, since mechanisms involved in the binding of AMPs to mammalian cells are largely unknown, their potential as novel anti-infective agents cannot be exploited yet. Following the reported interaction of Human Neutrophil Peptide 1 dimer (HNP1) with a low density lipoprotein receptor (LDLR), a computational study was conducted to discover their putative mode of interaction. State-of-the-art docking software produced... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5544508 Fri, 25 Nov 2011 05:00:00 +0100 5544508 http://www.medworm.com/index.php?rid=5544507&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22185498%26dopt%3DAbstract Authors: Simona LM, Laczkób I, Demcsáka A, Tótha D, Kotormán M, Fülöp L Abstract The formation of amyloid-like fibrils of α-chymotrypsin was studied in aqueous ethanol, methanol, tert-butanol, dimethylformamide and acetonitrile. Thioflavin T (ThT), Congo red (CR) and 1-anilino-8-naphthalenesulfonic acid (ANS) binding, turbidity, intrinsic fluorescence and far-UV circular dichroism measurements were employed to characterize the amyloid fibril formation. The greatest extent of fibril formation after incubation for 24 h at pH 7.0 and at 24 °C was in ethanol at 55%, in methanol and dimethylformamide (DMF) at 60-70% and in tert-butanol at 60-80%. The ANS binding and intrinsic fluorescence results showed that the hydrophobic residues are more solvent-exposed in the aggregated for... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5544507 Fri, 25 Nov 2011 05:00:00 +0100 5544507 http://www.medworm.com/index.php?rid=5544506&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22185499%26dopt%3DAbstract Authors: Yang Z, Lu Y, Liu J, Wang Y, Zhao X Abstract HspB8/Hsp22 is a functionally distinct small heat shock proteins (sHsp) and is preferentially expressed in brain, heart, skeletal, and smooth muscle. HspB8 is also associated with neuromuscular function and protein quality control by proteasomes in cardiac hypertrophy. However, the molecular properties in vitro and molecular oligomerization remain uncertain. In this investigation, the rat HspB8 gene was expressed in E.coli cells, and mature HspB8 protein was efficiently prepared. The chaperone-like activity of HspB8 in vitro was quantitatively analyzed by model substrates. Size exclusion chromatography revealed that HspB8 had polydisperse oligomers and underwent dynamic molecular transition in solution, existing in a dynamic equ... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5544506 Fri, 25 Nov 2011 05:00:00 +0100 5544506 http://www.medworm.com/index.php?rid=5544505&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22185500%26dopt%3DAbstract Authors: Liu L, Hu XZ, Liu XX, Wang Y, Li SB Abstract Identification on protein folding types is always based on the 27-class folds dataset, which was provided by Ding & Dubchak in 2001. But with the avalanche of protein sequences, fold data is also expanding, so it will be the inevitable trend to improve the existing dataset and expand more folding types. In this paper, we construct a multi-class protein fold dataset, which contains 3,457 protein chains with sequence identity below 35% and could be classified into 76 fold types. It was 4 times larger than Ding & Dubchak's dataset. Furthermore, our work proposes a novel approach of support vector machine based on optimal features. By combining motif frequency, low-frequency power spectral density, amino acid composition, th... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5544505 Fri, 25 Nov 2011 05:00:00 +0100 5544505 http://www.medworm.com/index.php?rid=5544504&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22185501%26dopt%3DAbstract Dynamical properties of steric zipper polymorphs formed by a IAPP-derived peptide. Protein Pept Lett. 2011 Nov 25; Authors: Stanzione F, Simone AD, Esposito1 L, Vitagliano1 L Abstract Understanding the molecular basis of neurodegenerative diseases have enormous implications for the development of effective therapeutic strategies. One of the most puzzling features of these pathologies is the occurrence of distinct strains, which are believed to be generated by alternative conformational transitions of the same protein/peptide. Very recently, it has been discovered that small model peptides are able to form alternative tightly packed assemblies (polymorphs) in the crystalline state. Intriguingly, it has been postulated that the different polymorphs of the same polypeptide seq... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5544504 Fri, 25 Nov 2011 05:00:00 +0100 5544504 http://www.medworm.com/index.php?rid=5544503&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22185502%26dopt%3DAbstract We report the stability of the two hyperthermophilic enzymes Sulfolobus solfataricus pyrimidine-specific nucleoside hydrolase (SsCU-NH) and Sulfolobus solfataricus purine-specific inosine-adenosine-guanosine nucleoside hydrolase (SsIAG-NH) against the denaturing action of temperature and guanidine hydrochloride by means of circular dichroism and fluorescence spectroscopy. The guanidine hydrochloride-induced unfolding is reversible for both enzymes as demonstrated by the analysis of the refolding process by activity assays and fluorescence measurements. The evidence that the denaturation of SsIAG-NH carried out in the presence of reducing agents proved to be reversible indicates that the presence of disulfide bonds interferes with the refolding process of this enzyme. Both enzymes are highl... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5544503 Fri, 25 Nov 2011 05:00:00 +0100 5544503 http://www.medworm.com/index.php?rid=5544502&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22185503%26dopt%3DAbstract In conclusion, similar to bromelain and papain, baupain hinders human platelets aggregation, probably through an unspecific cleavage in the Phe-Leu bond of PAR1. PMID: 22185503 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5544502 Fri, 25 Nov 2011 05:00:00 +0100 5544502 http://www.medworm.com/index.php?rid=5544501&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22185504%26dopt%3DAbstract Authors: Kabir SR, Islam MF, Alom MJ, Zubair MA, Absar N Abstract A lectin was purified (designated as TCSL) from the Snake guard seeds with molecular mass of 56±2 kDa containing two subunits (34±1 and 22±1 kDa.). TCSL exhibited high agglutination activity at the temperature range 30 to 70ºC and did not lose its activity between pH 3.0 to 12.0. The lectin was stable in the presence of denaturants and agglutinated mouse, goat, cow, chicken and human erythrocytes. TCSL did not show antifungal activity whereas it agglutinated six pathogenic bacteria and the lectin showed less toxicity against brine shrimp nauplii with the LC50 of 261±29 µg/ml. TCSL showed 28% and 72% inhibition against Ehrlich ascites carcinoma (EAC) cells in vivo in mice when administered 1 mg/kg/day and 2 mg/k... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5544501 Fri, 25 Nov 2011 05:00:00 +0100 5544501 http://www.medworm.com/index.php?rid=5544500&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22185505%26dopt%3DAbstract Predicting the classification of transcription factors by incorporating their binding site properties into a novel mode of Chou's pseudo amino acid composition. Protein Pept Lett. 2011 Nov 25; Authors: Ren LY, Zhang YS, Gutman I Abstract Transcription factors (TF) are proteins that control the first step of gene expression, the transcription of DNA into RNA sequences. The mechanism of transcriptional regulatory can be much better understood if the category of transcription factors is known. We developed a new method for predicting the classification of transcription factors by incorporating their binding site properties into a novel mode of Chou's pseudo amino acid composition. The properties include the length of TFBSs for a TF, a new_PWM value, the proportion of not conse... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5544500 Fri, 25 Nov 2011 05:00:00 +0100 5544500 http://www.medworm.com/index.php?rid=5544499&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22185506%26dopt%3DAbstract Authors: Chen C, Shen ZB, Zou XY Abstract A prior knowledge of protein structural class can provide useful information about its overall structure. So, it is vitally important to develop a computational prediction method for fast and accurately determining the protein structural class. In this paper, a dual-layer wavelet support vector machine (WSVM) is presented via the general form of Chou's pseudo amino acid composition, which is featured by introducing wavelet as a kernel and making decisions by the fusion from three individual classifiers. As a demonstration, the rigorous jackknife cross-validation tests were performed on two benchmark datasets, including the more challenging 25PDB dataset. Our success rates were reliable, and it has not escaped from our notice that the presen... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5544499 Fri, 25 Nov 2011 05:00:00 +0100 5544499 http://www.medworm.com/index.php?rid=5544498&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22185507%26dopt%3DAbstract Authors: Li LQ, Zhang Y, Zou LY, Zhoua Y, Zheng XQ Abstract Many proteins bear multi-locational characteristics, and this phenomenon is closely related to biological function. However, most of the existing methods can only deal with single-location proteins. Therefore, an automatic and reliable ensemble classifier for protein subcellular multi-localization is needed. We propose a new ensemble classifier combining the KNN (K-nearest neighbour) and SVM (support vector machine) algorithms to predict the subcellular localization of eukaryotic, Gram-negative bacterial and viral proteins based on the general form of Chou's pseudo amino acid composition, i.e., GO (gene ontology) annotations, dipeptide composition and AmPseAAC (Amphiphilic pseudo amino acid composition). This ensemble clas... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5544498 Fri, 25 Nov 2011 05:00:00 +0100 5544498 http://www.medworm.com/index.php?rid=5544497&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22185508%26dopt%3DAbstract Authors: Hayat M, Khan A Abstract Outer membrane proteins (OMPs) play important roles in cell biology. In addition, OMPs are targeted by multiple drugs. The identification of OMPs from genomic sequences and successful prediction of their secondary and tertiary structures is a challenging task due to short membrane-spanning regions with high variation in properties. Therefore, an effective and accurate silico method for discrimination of OMPs from their primary sequences is needed. In this paper, we have analyzed the performance of various machine learning mechanisms for discriminating OMPs such as: Genetic Programming, K-nearest Neighbor, and Fuzzy K-nearest Neighbor (Fuzzy K-NN) in conjunction with discrete methods such as: Amino acid composition, Amphiphilic Pseudo amino acid com... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5544497 Fri, 25 Nov 2011 05:00:00 +0100 5544497 http://www.medworm.com/index.php?rid=5544496&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22185509%26dopt%3DAbstract Authors: Cao JZ, Gu H Abstract Machine learning is a kind of reliable technology for automated subcellular localization of viral proteins within a host cell or virus-infected cell. One challenge is that the viral protein samples are not only with multiple location sites, but also class-imbalanced. The imbalanced dataset often decreases the prediction performance. In order to accomplish this challenge, this paper proposes a novel approach named imbalance-weighted multi-label K-nearest neighbor to predict viral protein subcellular location with multiple sites. The experimental results by jackknife test indicate that the presented algorithm achieves a better performance than the existing methods and has great potentials in protein science. PMID: 22185509 [PubMed - as supplied by p... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5544496 Fri, 25 Nov 2011 05:00:00 +0100 5544496 http://www.medworm.com/index.php?rid=5544495&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22185510%26dopt%3DAbstract Authors: Liao B, Xiang Q, Li D Abstract Protein structure information is very useful for the confirmation of protein function. The protein structural class can provide information for protein 3D structure analysis, causing the conformation of the protein overall folding type plays a significant part in molecular biology. In this paper, we focus on the prediction of protein structural class which was based on new feature representation. We extract features from the Chou-Fasman parameter, amino acid compositions, amino acids hydrophobicity features, polarity information and pair-coupled amino acid composition. The prediction result by the SVM classifier shows that our method is better than some others. PMID: 22185510 [PubMed - as supplied by publisher] (Source: Protein and Peptid... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5544495 Fri, 25 Nov 2011 05:00:00 +0100 5544495 http://www.medworm.com/index.php?rid=5358268&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22023113%26dopt%3DAbstract Authors: Zhou GP PMID: 22023113 [PubMed - in process] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5358268 Sat, 01 Oct 2011 04:00:00 +0100 5358268 http://www.medworm.com/index.php?rid=5240519&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21933114%26dopt%3DAbstract Authors: Sivakamasundari C, Nandakumar S, Nagaraj R Abstract The peptide sequence KLVFFAE that spans the region 16-22 in the amyloid peptide Aβ1-40 has the ability to form fibrils or nanotubes in aqueous medium, depending on the conditions of dissolution. Interaction between the phenylalanine residues is presumed to play an important role in the self-assembly of Aβ16-22. We have investigated the importance of these aromatic residues by substituting them with p-chloro-, p-fluoro- and p-methylphenylalanine. Nanostructures different from the parent peptide were obtained with the substituted analogs, both in methanol as well as aqueous conditions (pH 2 and pH 7). Concentration-dependent effects observed in methanol, suggest that intermediate states occur during fibrillation. A balanc... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5240519 Tue, 20 Sep 2011 04:00:00 +0100 5240519 http://www.medworm.com/index.php?rid=5240518&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21933115%26dopt%3DAbstract This study was aimed at evaluating the inhibitory effects of PBP in terms of NF-κB activation by using immunohistochemical and immunofluorescent technique in vitro and in vivo. IL-1β and TNF-α in serum were detected by method of ELISA. Immunofluorescent results showed that PBP inhibited NF-κB p65 translocation into nucleus. In vivo imaging showed that treatment with PBP decreased the enzyme labeling signal of NF-κB p65. Immunohistochemical staining revealed that PBP suppressed production of NF-κB p65 subunit in the joints and attenuated the productions of IL-1β and TNF-α in serum from AA. Moreover, NF- κB p65 nucleus translocation was prevented by simultaneous incubation with PBP and PGE(2) was decreased by PBP through a feedback cycle. We report the first confirmation of the mimo... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5240518 Tue, 20 Sep 2011 04:00:00 +0100 5240518 http://www.medworm.com/index.php?rid=5240517&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21933116%26dopt%3DAbstract Authors: Hashiguchi T, Ose T, Kubota M, Maita N, Kamishikiryo J, Maenaka K, Yanagi Y Abstract Measles virus (MV), one of the most contagious agents, infects immune cells using the signaling lymphocyte activation molecule (SLAM) on the cell surface. A complex of SLAM and the attachment protein, hemagglutinin (MV-H), has remained elusive due to the intrinsic handling difficulty including glycosylation. Furthermore, crystals obtained of this complex are either nondiffracting or poorly-diffracting. To solve this problem, we designed a systematic approach using a combination of the following techniques; (1) a transient expression system in HEK293SGnTI(-) cells, (2) lysine methylation, (3) structure-guided mutagenesis directed at better crystal packing, (4) Endo H treatment, (5) single-c... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5240517 Tue, 20 Sep 2011 04:00:00 +0100 5240517 http://www.medworm.com/index.php?rid=5240516&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21933117%26dopt%3DAbstract Authors: Marchot P, Chatonnet A PMID: 21933117 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5240516 Tue, 20 Sep 2011 04:00:00 +0100 5240516 http://www.medworm.com/index.php?rid=5240515&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21933118%26dopt%3DAbstract Authors: Vorobiev SM, Huang YJ, Seetharaman J, Xiao R, Acton TB, Montelione GT, Tong L Abstract Human retinoblastoma binding protein 9 (RBBP9) is an interacting partner of the retinoblastoma susceptibility protein (Rb). RBBP9 is a tumor-associated protein required for pancreatic neoplasia, affects cell cycle control, and is involved in the TGF-β signalling pathway. Sequence analysis suggests that RBBP9 belongs to the α/β hydrolase superfamily of enzymes. The serine hydrolase activity of RBBP9 is required for development of pancreatic carcinomas in part by inhibiting TGF-β antiproliferative signaling through suppressing Smad2/3 phosphorylation. The crystal structure of human RBBP9 confirms the α/β hydrolase fold, with a six-stranded parallel β-sheet flanked by α helixes. The... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5240515 Tue, 20 Sep 2011 04:00:00 +0100 5240515 http://www.medworm.com/index.php?rid=5240514&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21933119%26dopt%3DAbstract Authors: Bahl CD, Madden DR Abstract The Gram-negative bacterium Pseudomonas aeruginosa is an opportunistic pathogen that secretes a multitude of virulence factors during the course of infection. Among these is Cif, an epoxide hydrolase (EH) that reduces the functional localization of the cystic fibrosis transmembrane conductance regulator in epithelial cells. In addition to being the first reported EH virulence factor, Cif possesses unique sequence deviations from canonical EH motifs. Foremost among these is the substitution of a histidine for the second epoxide ring-opening tyrosine in the active site. To test the functional equivalence of the Tyr and His side chains at this position, we have generated the mutant Cif-H177Y. Structural analysis confirms that both the WT His and mu... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5240514 Tue, 20 Sep 2011 04:00:00 +0100 5240514 http://www.medworm.com/index.php?rid=5240513&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21933120%26dopt%3DAbstract Authors: Hirano K, Aya K, Matsuoka M, Ueguchi-Tanaka M Abstract Gibberellins (GAs) are tetracyclic, diterpenoid plant hormones, essential for many developmental processes in higher plants. Plants perceive GA through a nuclear-localized GA receptor, GA INSENSITIVE DWARF1 (GID1). From sequence similarity, it is suggested that GID1 evolved from a hormone-sensitive lipase (HSL), and recent x-ray crystallography of the GA-GID1 complex has given insights into how GID1 recognizes GA. Analyses of the GA signaling pathway in several plant species further suggest that the GID1-mediated GA signaling pathway emerged in the vascular plant lineage and since then regulation of GA recognition specificity seems to have been fine tuned to strictly regulate the on-off GA signal. PMID: 21933120 [P... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5240513 Tue, 20 Sep 2011 04:00:00 +0100 5240513 http://www.medworm.com/index.php?rid=5240512&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21933121%26dopt%3DAbstract Authors: De Jaco A, Comoletti D, Dubi N, Camp S, Taylor P Abstract The α/beta;-hydrolase fold family is perhaps the largest group of proteins presenting significant structural homology with divergent functions, ranging from catalytic hydrolysis to heterophilic cell adhesive interactions to chaperones in hormone production. All the proteins of the family share a common three-dimensional core structure containing the α/beta;-hydrolase fold domain that is crucial for proper protein function. Several mutations associated with congenital diseases or disorders have been reported in conserved residues within the α/beta;-hydrolase fold domain of cholinesterase-like proteins, neuroligins, butyrylcholinesterase and thyroglobulin. These mutations are known to disrupt the architecture of th... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5240512 Tue, 20 Sep 2011 04:00:00 +0100 5240512 http://www.medworm.com/index.php?rid=5240511&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21933122%26dopt%3DAbstract Authors: Halliday AC, Greenfield SA Abstract Acetylcholinesterase (AChE), a member of the α/β-hydrolase fold superfamily of proteins, is a serine hydrolase responsible for the hydrolysis of the well studied neurotransmitter acetylcholine (ACh). However, it is becoming clear that AChE has a range of actions other than this 'classical' role. Non-classical AChE functions have been identified in apoptosis, stress-responses, neuritogenesis, and neurodegeneration. Furthermore, these non-classical roles are attributable not only to the native protein, which appears to act as a mediary binding protein under a number of circumstances, but also to peptides cleaved from the parent protein. Peptides cleaved from AChE can act as independent signalling molecules. Here we discuss the implicatio... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5240511 Tue, 20 Sep 2011 04:00:00 +0100 5240511 http://www.medworm.com/index.php?rid=5240510&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21933123%26dopt%3DAbstract Authors: Vogel-Höpker A, Sperling LE, Layer PG Abstract Acetylcholinesterase (AChE) is a most remarkable protein, not only because it is one of the fastest enzymes in nature, but also since it appears in many molecular forms and is regulated by elaborate genetic networks. As revealed by sensitive histochemical procedures, AChE is expressed specifically in many tissues during development and in many mature organisms, as well as in healthy and diseased states. Therefore it is not surprising that there has been a long-standing search for additional, "non-classical" functions of cholinesterases (ChEs). In principle, AChE could either act non-enzymatically, e.g., exerting cell adhesive roles, or, alternatively, it could work within the frame of classic cholinergic systems, but in non-n... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5240510 Tue, 20 Sep 2011 04:00:00 +0100 5240510 http://www.medworm.com/index.php?rid=5240509&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21933124%26dopt%3DAbstract Authors: Giuseppe M, Luigia M, Elena P, Yan F, Luigi M Abstract The number of enzymes endowed with the capacity to catalyse other reactions than the main, physiological one, a feature that has been called promiscuity, is increasing at a fast pace. Promiscuity is a highly pervasive phenomenon that is present at each level of life complexity. For enzymes, promiscuity encompasses interesting aspects related to their physiological role, evolution and biotechnological applications. Herein, at first we will describe some general aspects of enzyme promiscuity and then we will report some examples from the a/b hydrolase superfamily of proteins, with particular emphasis to the hormone-sensitive lipase family. PMID: 21933124 [PubMed - as supplied by publisher] (Source: Protein and Peptid... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5240509 Tue, 20 Sep 2011 04:00:00 +0100 5240509 http://www.medworm.com/index.php?rid=5240508&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21933125%26dopt%3DAbstract Authors: Marchot P, Chatonnet A Abstract Genes coding for members of the alpha/beta hydrolase fold superfamily of proteins are present in all known genomes. Although there is no common and essential function performed by these proteins shared in all living organisms, this fold has been used for a number of diverse functions. The ancestry of both enzymatic and protein-protein interaction capability of this structural scaffold made it an important tinkering tool kit for protein function evolution. Recently, enzymes known since a long time have been found to have a second function in acting by promiscuously on alternative substrates, or to be true moonlighting proteins acting also as transporters, receptors, chaperones. The reverse situation has been encountered for adhesion proteins ... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5240508 Tue, 20 Sep 2011 04:00:00 +0100 5240508 http://www.medworm.com/index.php?rid=5240506&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21933126%26dopt%3DAbstract Authors: Vishwanatha TM, Narendra N, Sureshbabu VV Abstract One-pot click chemistry of N(α)-Boc-bromomethylketones, NaN(3) and propiolic acid affords N-Boc protected 1,4-disubstituted 1,2,3-β-ketotriazole acids in good to excellent yield. The use of CuI as catalyst and DMSO as solvent leads the click reaction to efficient, practical and column-free preparation of the title compounds. The utility of the resulting unnatural amino acids as building blocks to prepare triazole possessing peptidomimetics is also delineated. PMID: 21933126 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5240506 Tue, 20 Sep 2011 04:00:00 +0100 5240506 http://www.medworm.com/index.php?rid=5240505&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21933127%26dopt%3DAbstract Authors: Domènech A, Raynes JG, Arís A, Rodríguez EM, Bach A, Serrano A Abstract Serum Amyloid A3 (SAA3) protein is a member of a complex group of acute phase and constitutive proteins which have been related to several immune functions. Bovine milk SAA3 (M-SAA3) has been described to have a unique N-terminal TFLK motif responsible for up regulating mucin expression in the intestine lumen and therefore a protective gastrointestinal role. cDNA sequences encoding the protein goat M-SAA3 were successfully cloned from milk, mammary gland tissue and liver, expressed despite observed toxicity and purified as a soluble protein. Sequence analyses of the milk and liver derived forms revealed a non mammary-restricted common N-terminal TFLR motif, unlike that described for bovine M-SAA3. S... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5240505 Tue, 20 Sep 2011 04:00:00 +0100 5240505 http://www.medworm.com/index.php?rid=5240504&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21933128%26dopt%3DAbstract Authors: Staunton L, Ohlendieck K Abstract The sarcoplasmic reticulum from skeletal muscle constitutes an elaborate membrane system that contains a considerable number of integral and very large proteins that exist in highly complex supramolecular clusters. Conventional proteomics using two-dimensional gel electrophoresis greatly underestimates the presence of these proteins. Here, we have applied one-dimensional gradient gels and on-membrane digestion to overcome this technical problem. Mass spectrometric analysis has determined the presence of 31 distinct protein species in the sarcoplasmic reticulum, including key Ca(2+)-handling proteins such as the ryanodine receptor, Ca(2+)-ATPase, calsequestrin and sarcalumenin. Immunoblotting confirmed the relative position of these Ca(2+)-... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5240504 Tue, 20 Sep 2011 04:00:00 +0100 5240504 http://www.medworm.com/index.php?rid=5240503&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21933129%26dopt%3DAbstract Authors: Ponmariappan S, Jain S, Sijoria R, Tomar A, Kumar O Abstract Botulism is a neuroparalytic disease caused by Clostridium botulinum, which produces seven (A-G) neurotoxins (BoNTs). The mouse bioassay is the gold standard for the detection of botulinum neurotoxins, however it requires at least 3-4 days for completion. Most of the studies were carried out in botulinum toxin A and less on type B. Attempts have been made to develop an ELISA based detection system, which is potentially an easier and more rapid method of botulinum neurotoxin detection. In the present study, the synthetic BoNT/B LC gene was constructed using PCR overlapping primers, cloned in a pET28a+ vector and expressed in E. coli BL21DE3. The maximum yield of recombinant proteins was optimized after 16 hrs of p... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5240503 Tue, 20 Sep 2011 04:00:00 +0100 5240503 http://www.medworm.com/index.php?rid=5240502&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21933130%26dopt%3DAbstract In this study, the rice heterotrimeric G protein subunits α (Gα) and β (Gβ) were purified by affinity chromatography using anti-Gα and -Gβ antibodies and SDS-PAGE. Six and seven peptides, respectively, were identified by mass spectrometry and identified as the translation products of the Gα gene RGA1 and Gβ gene RGB1. During purification, the subunits dissociated easily from the G protein complex and from each other. PMID: 21933130 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5240502 Tue, 20 Sep 2011 04:00:00 +0100 5240502 http://www.medworm.com/index.php?rid=5240501&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21933131%26dopt%3DAbstract Authors: Khalili-Hezarjaribi H, Yousefi R, Moosavi-Movahedi AA Abstract As major chaperone of eye lens, alpha-crystallin (α-Crs) is responsible for the transparency and refractive power of this region by preventing denaturation and precipitation of other proteins. As shown previously, cataract formation was positively associated with high salt intake and the elevation of blood sugar level. Here the effect of both temperature and ionic strength were studied on structure and chaperoning function of glycated and non-glycated α-Crs. While chaperone activity of these proteins was increased as function of temperature elevation, in the presence of sodium salt (0-160 mM), it was significantly decreased. As shown by fluorescence and circular dicroism (CD) instruments, the salt induced str... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5240501 Tue, 20 Sep 2011 04:00:00 +0100 5240501 http://www.medworm.com/index.php?rid=5240500&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21933132%26dopt%3DAbstract Authors: Jensen JM, Ernst HA, Wang X, Hald H, Ditta AC, Ismat F, Rahman M, Mirza O Abstract Proton-dependent oligopeptide transporters (POTs) are secondary active symporters that utilize the proton gradient to drive the inward translocation of di- and tripeptides. We have mutated two highly conserved membrane embedded glutamate residues(Glu20 and Glu388) in the E. coli POT YjdL to probe their possible functional roles, in particular if they were involved/implicated in recognition of the substrate N-terminus. The mutants (Glu20Asp, Glu20Gln, Glu388Asp, and Glu388Gln) were tested for substrate uptake, which indicated that both the negative charge and the side chain length were important for function. The IC(50) values of dipeptides with lack of or varying N-terminus (Ac-Lys, Gly-Lys,... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5240500 Tue, 20 Sep 2011 04:00:00 +0100 5240500 http://www.medworm.com/index.php?rid=5240499&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21933133%26dopt%3DAbstract Authors: Pinedo M, Regente M, Elizalde M, Quiroga IY, Pagnussat LA, Jorrín-Novo J, Maldonado A, de la Canal L Abstract Extracellular proteins from sunflower seedlings were analyzed by electrophoresis followed by peptide mass fingerprinting. Tentative identification revealed novel proteins for this crop. A significant number of those proteins were not expected to be extracellular because they lacked the typical signal peptide responsible for secretion. In silico analysis showed that some members of this group presented the characteristic disordered structures of certain non-classical and leaderless mammalian secretory proteins. Among these proteins, a putative jacalin-related lectin (Helja) with a mannose binding domain was further isolated from extracellular fluids by mannose-affi... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5240499 Tue, 20 Sep 2011 04:00:00 +0100 5240499 http://www.medworm.com/index.php?rid=5240498&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21933134%26dopt%3DAbstract Authors: Wang R, Zhou S, Peng X, Zhou XW, Xie ZQ, Wang Y, Mo W, Yu M Abstract TACI is a member of the tumor necrosis factor receptor superfamily and serves as a key regulator of B cell function. The extracellular domain of a typical TNFR contains multiple copies of CRD, which bind in the monomer-monomer interfaces of a trimeric ligand. TACI binds to two ligands, APRIL and BAFF, with high affinity and contains two CRD in its extracellular regions, while BCMA and BR3, contain a single or partial CRD for binding the two ligands. However, TACI can be classified as a single CRD receptor because the amino-terminal CRD1 doesn't contribute to ligand binding. To obtain a new variant of TACI possessing higher affinities for binding, we fused a repeat sequence of CRD2 to the N-terminus of the... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5240498 Tue, 20 Sep 2011 04:00:00 +0100 5240498 http://www.medworm.com/index.php?rid=5240496&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21933135%26dopt%3DAbstract Authors: Charbonneau DM, Meddeb-Mouelhi F, Beauregard M Abstract The novel thermostable carboxylesterase EstGtA2 from G. thermodenitrificans (accession no. JN031579) was functionally expressed and purified using an N-terminal fusion tag peptide. We recently reported general properties of the recombinant enzyme. Here we report preliminary data on thermal stability of EstGtA2 and of its tagged form. Conformational stability was investigated using circular dichroism and correlated with residual activity measurements using a colorimetric assay. The tag peptide had no considerable impact on the apparent melting temperature: T(m) value = 64.8°C (tagged) and 65.7°C (cleaved) at pH 8. After thermal unfolding, the tag-free enzyme rapidly recovered initial activity at 25°C (1.2 Umg(-1)), ... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5240496 Tue, 20 Sep 2011 04:00:00 +0100 5240496 http://www.medworm.com/index.php?rid=5240495&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21933136%26dopt%3DAbstract In this study, a new method is proposed to predict PPIs using a comprehensive set of 930 features based only on sequence information, these features measure the interactions between residues a certain distant apart in the protein sequences from different aspects. To achieve better performance, the principal component analysis (PCA) is first employed to obtain an optimized feature subset. Then, the resulting 67-dimensional feature vectors are fed to Support Vector Machine (SVM). Experimental results on Drosophila melanogaster and Helicobater pylori datasets show that our method is very promising to predict PPIs and may at least be a useful supplement tool to existing methods. PMID: 21933136 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5240495 Tue, 20 Sep 2011 04:00:00 +0100 5240495 http://www.medworm.com/index.php?rid=5240494&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21933137%26dopt%3DAbstract Authors: Zhang H, Shi H, Hanlon M Abstract As an alternative to X-ray crystallography, nuclear magnetic resonance (NMR) has also emerged as the method of choice for studying both protein structure and dynamics in solution. However, little work using computational models such as Gaussian network model (GNM) and machine learning approaches has focused on NMR-derived proteins to predict the residue flexibility, which is represented by the root mean square deviation (RMSD) with respect to the average structure. We provide a large-scale comparison of computational models, including GNM, parameter-free GNM and several linear regression models using local solvent exposures as inputs, based on a dataset of 1609 protein chains whose structures were resolved by NMR. The result again confirme... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5240494 Tue, 20 Sep 2011 04:00:00 +0100 5240494 http://www.medworm.com/index.php?rid=5240637&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21919851%26dopt%3DAbstract Authors: Wu LC, Hsieh PH, Horng JT, Jou YJ, Lin CD, Cheng KF, Lin CW, Chen SY Abstract Mass spectrometry biomarker discovery may assist patient's diagnosis in time and realize the characteristics of new diseases. Our previous work built a preprocess method called HHTmass which is capable of removing noise, but HHTmass only a proof of principle to be peak detectable and did not tested for peak reappearance rate and used on medical data. We developed a modified version of biomarker discovery method called Enhance HHTMass (E-HHTMass) for MALDI-TOF and SELDI-TOF mass spectrometry data which improved old HHTMass method by removing the interpolation and the biomarker discovery process. E-HHTMass integrates the preprocessing and classification functions to identify significant peaks. The ... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5240637 Thu, 15 Sep 2011 04:00:00 +0100 5240637 http://www.medworm.com/index.php?rid=5240636&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21919852%26dopt%3DAbstract Authors: Huang T, Cai YD, Chen L, Hu L, Kong XY, Li YX, Chou KC Abstract Induced pluripotent stem cells have displayed great potential in disease investigation and drug development applications. However, selection of reprogramming factors in each cell type or disease state is both expensive and time consuming. To deal with this kind of situation, a fast computational framework was developed by optimize the reprogramming factors via the protein interaction network and gene functional profiles. It can be used to select reprogramming factors from millions of possibilities. It is anticipated that the novel approach will become a very useful tool for both basic research and drug development. PMID: 21919852 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5240636 Thu, 15 Sep 2011 04:00:00 +0100 5240636 http://www.medworm.com/index.php?rid=5240635&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21919853%26dopt%3DAbstract Authors: Peng CR, Lu WC, Niu B, Li YJ, Hu LL Abstract As many diseases like high cholesterol are referred to lipid metabolism, studying the lipid metabolic pathway has a positive effect on finding the knowledge about interactions between different elements within high complex living systems. Here, we employed a typical ensemble learning method, Bagging learner, to study and predict the possible sub lipid metabolic pathway of small molecules based on physical and chemical features of the compounds. As a result, jackknife cross validation test and independent set test on the model reached 89.85% and 91.46%, respectively. Therefore, our predictor may be used for finding the new compounds which participate in lipid metabolic procedures. PMID: 21919853 [PubMed - as supplied by publi... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5240635 Thu, 15 Sep 2011 04:00:00 +0100 5240635 http://www.medworm.com/index.php?rid=5240633&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21919854%26dopt%3DAbstract Authors: Chen L, Cai YD, Shi XH, Huang T Abstract Given a compounds-forming system, i.e., a system consisting of some compounds and their relationship, can it form a biologically meaningful pathway? It is a fundamental problem in systems biology. Nowadays, a lot of information on different organisms, at both genetic and metabolic levels, has been collected and stored in some specific databases. Based on these data, it is feasible to address such an essential problem. Metabolic pathway is one kind of compounds-forming systems and we analyzed them in yeast by extracting different (biological and graphic) features from each of the 13,736 compounds-forming systems, of which 136 are positive pathways, i.e., known metabolic pathway from KEGG; while 13,600 were negative. Each of these com... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5240633 Thu, 15 Sep 2011 04:00:00 +0100 5240633 http://www.medworm.com/index.php?rid=5240625&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21919855%26dopt%3DAbstract In this study, we developed a novel method for the prediction of enzyme-small molecules interactions based on machine learning approach. The biochemical and physicochemical description of proteins and the functional group composition of small molecules are used for representing enzyme-small molecules pairs. Tested by jackknife cross-validation, our predictor achieved an overall accuracy of 87.47%, showing an acceptable efficiency. The 39 features selected by feature selection were analyzed for further understanding of enzyme-small molecule interactions. PMID: 21919855 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5240625 Thu, 15 Sep 2011 04:00:00 +0100 5240625 http://www.medworm.com/index.php?rid=5240590&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21919856%26dopt%3DAbstract Authors: Yi XF, He ZS, Chou KC, Kong XY Abstract The DNA of all eukaryotic organisms is packaged into nucleosomes (a basic repeating unit of chromatin). A nucleosome consists of histone octamer wrapped by core DNA and linker histone H1 associated with linker DNA. It has profound effects on all DNA-dependent processes by affecting sequence accessibility. Understanding the factors that influence nucleosome positioning has great help to the study of genomic control mechanism. Among many determinants, the inherent DNA sequence has been suggested to have a dominant role in nucleosome positioning in vivo. Here, we used the method of minimum redundancy maximum relevance (mRMR) feature selection and the nearest neighbor algorithm (NNA) combined with the incremental feature selection (IFS) ... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5240590 Thu, 15 Sep 2011 04:00:00 +0100 5240590 http://www.medworm.com/index.php?rid=5240550&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21919857%26dopt%3DAbstract Authors: He Z, Shi XH, Kong XY, Zhu YB, Chou KC Abstract Phosphorylation is one of the most important post-translational modifications, and the identification of protein phosphorylation sites is particularly important for studying disease diagnosis. However, experimental detection of phosphorylation sites is labor intensive. It would be beneficial if computational methods are available to provide an extra reference for the phosphorylation sites. Here we developed a novel sequence-based method for serine, threonine, and tyrosine phosphorylation site prediction. Nearest Neighbor algorithm was employed as the prediction engine. The peptides around the phosphorylation sites with a fixed length of thirteen amino acid residues were extracted via a sliding window along the protein chains ... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5240550 Thu, 15 Sep 2011 04:00:00 +0100 5240550 http://www.medworm.com/index.php?rid=5240549&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21919858%26dopt%3DAbstract Authors: Cai L, Huang W, Chou KC Abstract Both CYP17 and UGT2B17 are suggested to be potential risk factors of prostate cancer (PCa). To date, many studies have evaluated the relationship between CYP17 T-34C and UGT2B17 Del polymorphisms and Prostate cancer with conflicting results. Here, we performed comprehensive meta-analyses of over 25 studies, including results from about 17,000 subjects on the association of CYP17 T-34C and UGT2B17 Del polymorphisms with Prostate cancer. Overall, no significant associations between CYP17 T-34C polymorphism and Prostate cancer risk were found for T versus C (P=0.63), TT versus CC (P=0.52), TT+TC versus CC (P=0.40) or TT versus TC+CC (P=0.98), though there was a marginally significant association with the UGT2B17 Del polymorphism under Del/Del ... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5240549 Thu, 15 Sep 2011 04:00:00 +0100 5240549 http://www.medworm.com/index.php?rid=5240547&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21919859%26dopt%3DAbstract In this study, a web-server called SCYPPred was developed for predicting human cytochrome P450 SNPs (Single Nucleotide Polymorphisms) based on the SVM flanking sequence method; SCYPPred can rapidly yield the desired results by using the amino acid sequences information alone. The web-server is accessible to the public at http://snppred.sjtu.edu.cn. Hopefully SCYPPred could be a useful bioinformatics tool for elucidating the mutation probability of a specific CYP450 enzyme. PMID: 21919859 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5240547 Thu, 15 Sep 2011 04:00:00 +0100 5240547 http://www.medworm.com/index.php?rid=5240545&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21919860%26dopt%3DAbstract Authors: Pugalenthi G, Kandaswamy KK, Chou KC, Vivekanandan S, Kolatkar P Abstract Prediction of protein structure from its amino acid sequence is still a challenging problem. The complete physicochemical understanding of protein folding is essential for the accurate structure prediction. Knowledge of residue solvent accessibility gives useful insights into protein structure prediction and function prediction. In this work, we propose a random forest method, RSARF, to predict residue accessible surface area from protein sequence information. The training and testing was performed using 120 proteins containing 22006 residues. For each residue, buried and exposed state was computed using five thresholds (0%, 5%, 10%, 25%, and 50%). The prediction accuracy for 0%, 5%, 10%, 25%, and 50... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5240545 Thu, 15 Sep 2011 04:00:00 +0100 5240545 http://www.medworm.com/index.php?rid=5240539&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21919861%26dopt%3DAbstract Authors: Mizianty MJ, Kurgan LA Abstract Relatively low success rates of X-ray crystallography, which is the most popular method for solving proteins structures, motivate development of novel methods that support selection of tractable protein targets. This aspect is particularly important in the context of the current structural genomics efforts that allow for a certain degree of flexibility in the target selection. We propose CRYSpred, a novel in-silico crystallization propensity predictor that uses a set of 15 novel features which utilize a broad range of inputs including charge, hydrophobicity, and amino acid composition derived from the protein chain, and the solvent accessibility and disorder predicted from the protein sequence. Our method outperforms seven modern crystalliza... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5240539 Thu, 15 Sep 2011 04:00:00 +0100 5240539 http://www.medworm.com/index.php?rid=5240524&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21919862%26dopt%3DAbstract In this study, we used a 20-2 feedforward backpropagation neural network to build the relationship between information obtained from primary structure of cellulase with optimal pH and temperature to predict the optimal pH and temperature in cellulases. The results show that the amino-acid distribution probability representing the primary structure of cellulase can predict both optimal pH and temperature, whereas various properties of amino acids related to the primary structure cannot do so. PMID: 21919862 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5240524 Thu, 15 Sep 2011 04:00:00 +0100 5240524 http://www.medworm.com/index.php?rid=5240523&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21919863%26dopt%3DAbstract Authors: Hu LL, Feng KY, Gu L, Liu XJ Abstract Information of protein quaternary structure can help to understand the biological functions of proteins. Because wet-lab experiments are both time-consuming and costly, we adopt a novel computational approach to assign proteins into 10 kinds of quaternary structures. By coding each protein using its biochemical and physicochemical properties, feature selection was carried out using Incremental Feature Selection (IFS) method. The thus obtained optimal feature set consisted of 97 features, with which the prediction model was built. As a result, the overall prediction success rate is 74.90% evaluated by Jackknife test, much higher than the overall correct rate of a random guess 10% (1/10). The further feature analysis indicates that prote... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5240523 Thu, 15 Sep 2011 04:00:00 +0100 5240523 http://www.medworm.com/index.php?rid=5240522&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21919864%26dopt%3DAbstract Authors: Wang K, Hu L, Shi X, Dong Y, Li H, Wen T Abstract It is well known that protein subcellular localizations are closely related to their functions. Although many computational methods and tools are available from Internet, it is still necessary to develop new algorithms in this filed to gain a better understanding of the complex mechanism of plant subcellular localization. Here, we provide a new web server named PSCL for plant protein subcellular localization prediction by employing optimized functional domains. After feature optimization, 848 optimal functional domains from InterPro were obtained to represent each protein. By calculating the distances to each of the seven categories, PSCL showing the possibilities of a protein located into each of those categories in ascend... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5240522 Thu, 15 Sep 2011 04:00:00 +0100 5240522 http://www.medworm.com/index.php?rid=5240521&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21919865%26dopt%3DAbstract Authors: Wu ZC, Xiao X, Chou KC Abstract By introducing the "multi-layer scale", as well as hybridizing the information of gene ontology and the sequential evolution information, a novel predictor, called iLoc-Gpos, has been developed for predicting the subcellular localization of Gram positive bacterial proteins with both single-location and multiple-location sites. For facilitating comparison, the same stringent benchmark dataset used to estimate the accuracy of Gpos-mPLoc was adopted to demonstrate the power of iLoc-Gpos. The dataset contains 519 Gram-positive bacterial proteins classified into the following four subcellular locations: (1) cell membrane, (2) cell wall, (3) cytoplasm, and (4) extracell; none of proteins included has ≥25%pairwise sequence identity to any other i... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5240521 Thu, 15 Sep 2011 04:00:00 +0100 5240521 http://www.medworm.com/index.php?rid=5240520&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21919866%26dopt%3DAbstract Protein Pept Lett. 2011 Sep 15; Authors: Cai Y PMID: 21919866 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5240520 Thu, 15 Sep 2011 04:00:00 +0100 5240520 http://www.medworm.com/index.php?rid=5147361&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21838696%26dopt%3DAbstract In this study, to develop novel short antibiotic peptides useful as therapeutic drugs, an analogue was designed to possess increased hydrophobicity by Trp substitution in position 2 region of HP (4-16). Synthetic HP (4-16)-W showed an enhanced antimicrobial and antitumor activity. The antimicrobial activity of this peptide and others was measured by their growth inhibitory effect upon S. aureus, B. subtilis, S. epidermidis, E. coli, S. typimurium, P. aeruginosa, C. albicans, T. beigelii and S. cerevisiae. None of the peptides exhibited hemolytic activity against human erythrocyte cells except melittin as a positive control. Its antibiotic activity suggests that HP (4-16)-W is an excellent candidate as a lead compound for the development of novel antibiotic agents. PMID: 21838696 [PubMe... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5147361 Sun, 14 Aug 2011 23:00:00 +0100 5147361 http://www.medworm.com/index.php?rid=5147360&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21838697%26dopt%3DAbstract Authors: Sharma K, Gupta P, Singh AK, Gopalan N, Dhaked RK, Rao PV Shiga toxins are one of the very potent agents for causing dysentery, diarrhoea and haemolytic uremic syndrome with very low LD50. For better understanding of their biology, detection and neutralization, the components of toxins are needed to be expressed and purified in bulk amounts. However, following traditional expression procedures, this task is very tedious as the yield of the toxin is very low. In this manuscript, we have described the optimization of media for enhanced production of recombinant Shiga toxin B (rStx-B) chain protein in Escherichia coli. This protein is known to have neutralization ability against shiga toxins. Furthermore, fed-batch cultivation process in E. coli was also developed in the optimize... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5147360 Sun, 14 Aug 2011 23:00:00 +0100 5147360 http://www.medworm.com/index.php?rid=5138914&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21838698%26dopt%3DAbstract In this study, icarapin of Asian honey bee was cloned and sequenced. By in silico screening, S198 was found to be the potential antigenic site. This site was changed to cysteine and coupled with PEG(5K). Compared to the wild type icarapin and the S198C variant, PEGylated S198C variant induced lower level of IgG and IgE antibodies in mice, showing that it is indeed located in an antigenic site. Our work may be generalized to other proteins for the discovery of antigenic sites and the reduction of antigenicity. PMID: 21838698 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5138914 Sun, 14 Aug 2011 23:00:00 +0100 5138914 http://www.medworm.com/index.php?rid=5138863&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21838699%26dopt%3DAbstract Authors: Liu D, Wang X, Chen Z Rare earth elements (REEs), which include 17 elements in the periodic table, share chemical properties related to a similar external electronic configuration. REEs enriched fertilizers have been used in China since the 1980s. REEs could enter the cell and cell organelles, influence plant growth, and mainly be bound with the biological macromolecules. REE-binding proteins have been found in some plants. In addition, the chlorophyll activities and photosynthetic rate can be regulated by REEs. REEs could promote the protective function of cell membrane and enhance the plant resistance capability to stress produced by environmental factors, and affect the plant physiological mechanism by regulating the Ca(2+) level in the plant cells. The focus of present rev... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5138863 Sun, 14 Aug 2011 23:00:00 +0100 5138863 http://www.medworm.com/index.php?rid=5138816&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21838700%26dopt%3DAbstract In this study, GLP-1 analogues with modifications in amino acid site 8, 22 and 23 were synthesized using solid phase peptide synthesis. Resistance of these analogues to DPP-IV cleavage was investigated in vitro by incubation of the peptides with DPP-IV or human plasma. Glucoregulating efficacy of the analogues was evaluated in normal Kunming mice using intraperitoneal glucose tolerance model. Glucose lowering effect of combination therapy (analogue plus Vildagliptin) has also been studied. In vitro studies showed that the modified analogues were much more stable than native GLP-1 (nearly 100% of the peptide keep intact after 4 h incubation). In vivo biological activity evaluation revealed that His8-EEE (the most potent GLP-1 analogues in this study) exhibited significantly improved glycemi... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5138816 Sun, 14 Aug 2011 23:00:00 +0100 5138816 http://www.medworm.com/index.php?rid=5138795&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21838701%26dopt%3DAbstract Authors: Khemtémourian L, Desbenoit N, Mahesh P, Chatterjee S, Deschemin JC, Vaulont S, Tomas A, Sari MA, Artaud I Hepcidin, a 25 amino acid peptide hormone containing a complex network of four disulfide bonds is the hormone regulator of iron homeostasis. Three bridges synthetic peptide analogs have been prepared following two synthetic strategies and two oxidation procedures: i) a microwave-assisted solid phase synthesis followed by air oxidation of the six free cysteines ii) a manual solid phase synthesis followed by stepwise deprotection and oxidation of cysteine pairs. All the peptides with different connectivities have been characterized by MALDI ToF spectrometry, and tested for their ability to degrade the cellular iron exporter, ferroportin. While linear peptides are inactive, ... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5138795 Sun, 14 Aug 2011 23:00:00 +0100 5138795 http://www.medworm.com/index.php?rid=5089329&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21787278%26dopt%3DAbstract Authors: Hu X, Gao C, Tan C, Zhang C, Zhang H, Li S, Liu H, Jiang Y A series of novel compounds with N-phosphoryl peptide modification at the C-4 position on podophyllotoxin were synthesized and evaluated for their cytotoxicity in vitro against K562 cell lines. Among these compounds 5c, 5f and 5k exhibited better cytotoxicity (IC(50) = 5.5 µM, 2.1 µM, and 3.1 µM, respectively) than podophyllotoxin and etoposide. Further study on compound 5f using flow cytometry analysis indicated that the anti-tumor effect might be due to the induction of apoptosis. PMID: 21787278 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5089329 Sun, 24 Jul 2011 23:00:00 +0100 5089329 http://www.medworm.com/index.php?rid=5089328&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21787279%26dopt%3DAbstract We report here that the phenothiazine trifluoperazine non-competitively inhibits Plasmodium falciparum CDPK4 in the micromolar range while other calmodulin antagonists only marginally affect the enzyme activity, and we propose the inhibition mechanism. Our results demonstrate that selective enzyme inhibition is achievable by targeting its calmodulin-like domain. This observation could be exploited for the discovery of innovative phenothiazine-based CDPK inhibitors of potential medical interest. PMID: 21787279 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5089328 Sun, 24 Jul 2011 23:00:00 +0100 5089328 http://www.medworm.com/index.php?rid=5089327&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21787280%26dopt%3DAbstract Authors: Singh RK, Srivastava VC, Singh UP The superoxide anion radical is a highly reactive toxic species produced during the metabolic processes. A number of copper (II) complexes with amino acids and peptides are known to show superoxide dismutase (SOD) like activity. The design and application of synthetic low molecular weight metal complexes as SOD mimics have received considerable attention during the last decade. A variety of di- and tri-peptides containing histidyl residue in different positions have been employed to bind Cu(II) and to show the activity. But reports on Cu(II) complex with tetra-peptide having histidine amino acid in this regard are limited. As the HGGGW peptide having His at its N-terminal is reported to be a potential moiety for Cu(2+) binding, in the present ... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5089327 Sun, 24 Jul 2011 23:00:00 +0100 5089327 http://www.medworm.com/index.php?rid=5089326&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21787281%26dopt%3DAbstract Authors: Li N, Tan L, Yan L, Shi G, Wang Z, Liao Z Mussels Mytilus coruscus can adhere to various solid surface in the presence of moisture. Mussel foot protein-3 (mfp-3) has been suggested as the main adhesive protein in the plaques closest to the adhesion interface and been the focus of substantial biomaterials development research within the last decade. The byssal plaques of M. coruscus were accumulated and variants of a family known as mcofp3 (Mytilus coruscus foot protein 3) were purified from acetic acid/urea extracts of plaques, with their N-terminal sequences determined thereafter. The cDNA sequence coding for the mcofp3 precursor was obtained from M. coruscus foot cDNA library. These precursors contain a putative signal peptide of 24 residues, a mature peptide sequence of 41-... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5089326 Sun, 24 Jul 2011 23:00:00 +0100 5089326 http://www.medworm.com/index.php?rid=5089325&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21787282%26dopt%3DAbstract Authors: Liu XL, Lu JL, Hu XH Comprehensive knowledge of thermophilic mechanisms about some organisms whose optimum growth temperature (OGT) ranges from 50 to 80 °C degree plays a major role for helping to design stable proteins. How to predict function-unknown proteins to be thermophilic is a long but not fairly resolved problem. Chaos game representation (CGR) can investigate hidden patterns in protein sequences, and also can visually reveal their previously unknown structures. In this paper, using the general form of pseudo amino acid composition to represent protein samples, we proposed a novel method for presenting protein sequence to a CGR picture using CGR algorithm. A 24-dimensional vector extracted from these CGR segments and the first two PCA features are used to classify th... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5089325 Sun, 24 Jul 2011 23:00:00 +0100 5089325 http://www.medworm.com/index.php?rid=5089324&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21787283%26dopt%3DAbstract Authors: Mukai K, Shimizu T, Igarashi J Heme-regulated eukaryotic initiation factor 2α kinase (HRI) functions under conditions of heme shortage caused by blood diseases such as erythropoietic protoporphyria and β-thalassemia, and retains the heme:globin ratio at 1:1 by sensing the heme concentration in reticulocytes. This HRI function is regulated by various factors including autophosphorylation and protein-protein interactions. A heat-shock protein controls HRI function; however, the molecular mechanism of catalytic regulation of HRI by the heat-shock protein is unclear. In the present study, we examined the interactions of HRI with a heat-shock protein, Hsp90, under various conditions, using a pull-down assay and measuring catalytic activity. It was found that [1] an interaction be... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5089324 Sun, 24 Jul 2011 23:00:00 +0100 5089324 http://www.medworm.com/index.php?rid=5038917&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21728988%26dopt%3DAbstract Authors: Lin J, Wang Y For a protein, an important characteristic is its location or compartment in a cell. This is because a protein has to be located in its proper position in a cell to perform its biological functions. Therefore, predicting protein subcellular location is an important and challenging task in current molecular and cellular biology. In this paper, based on AdaBoost.ME algorithm and Chou's PseAAC (pseudo amino acid composition), a new computational method was developed to identify protein subcellular location. AdaBoost.ME is an improved version of AdaBoost algorithm that can directly extend the original AdaBoost algorithm to deal with multi-class cases without the need to reduce it to multiple two-class problems. In some previous studies the conventional amino acid com... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5038917 Mon, 04 Jul 2011 23:00:00 +0100 5038917 http://www.medworm.com/index.php?rid=5038916&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21728989%26dopt%3DAbstract Authors: Panda P, Suar M, Singh D, Pandey SM, Chaturvedi MM, Purohit JS Glutamate dehydrogenase (GDH) enzyme is recently being reported to be present in the nucleus in addition to the mitochondria in a number of organisms. Here we investigated the distribution of GDH in liver and brain tissues of chicken. Polyclonal anti-GDH antibody against bovine GDH was raised by us, which was later shown to be immune-reactive to chicken GDH. The nuclear and the mitochondrial extracts from liver and brain tissues of chicken were made as described. By quantitative immunoreactivity, it was revealed that the nuclear GDH expressed in comparable efficiencies in the liver and brain. However, the activity of the brain nuclear GDH was lower than the liver counterparts. The allosteric regulation pattern for ... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5038916 Mon, 04 Jul 2011 23:00:00 +0100 5038916 http://www.medworm.com/index.php?rid=5038915&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21728990%26dopt%3DAbstract Authors: Zhang XC, Wang WD, Wang JS, Pan JC, Zou GL Cyclophilin A (CyPA) is a cytosolic receptor of immunosuppressive drug cyclosporin A (CsA) which possesses peptidyl-prodyl cis/trans isomerase (PPIase) activity. The recombinant human CyPA (rhCyPA) gene has been expressed in E. coli M15. Purification was performed using salting-out, as well as Sephacryl S-100 and DEAE-Sepharose CL-6B column chromatography. The molecular weight is about 18 kDa, confirmed by SDS-PAGE and mass spectrum. The results of Native-PAGE and immunoblotting showed the existence of three bands, which agreed well with the gel filtration results. The molecular mass of the three bands determined via CTAB gel electrophoresis and SDS-PAGE (rhCyPA cross-linked with glutaraldehyde) was 18 kDa, 36 kDa and 54 kDa respectiv... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5038915 Mon, 04 Jul 2011 23:00:00 +0100 5038915 http://www.medworm.com/index.php?rid=5038914&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21728991%26dopt%3DAbstract Authors: Girzal VU, Neelagund S, Krishnappa M Ganoderma lucidum is known for its high medicinal value, clinically used in treatment for various diseases. We have selected this mushroom for isolation of novel bioactive lectin. The isolation procedure comprised of ion-exchange chromatography on DEAE- cellulose and affinity chromatography on Affi-gel blue gel. Purified lectin was monomer with a molecular mass of 15 kDa, determined by SDS-PAGE, Gel filtration, MALDI-ToF. It showed hemagglutinating activity against both human and animal erythrocytes. The hemagglutination activity was not inhibited by simple sugars but inhibited by glycoproteins. The activity was maximal at pH range 4.0-9.0 and at temperature up to 60°C. The hemagglutination activity was stable even in the presence of 10mM ... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5038914 Mon, 04 Jul 2011 23:00:00 +0100 5038914 http://www.medworm.com/index.php?rid=5038913&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21728992%26dopt%3DAbstract In this study, physicochemical scale (P-scale), was recruited as a novel set of physicochemical descriptors derived from component analysis on four short of physicochemical properties variables (hydrophobic, electronic, steric and hydrogen bond contribution) of 20 coded amino acids, By using partial least squares (PLS), we applied P-scale for the study of quantitative structure-activity relationship models (QASRs) on three angiotensin I converting enzyme (ACE) inhibitory peptides datasets (58 dipeptides, 55 tripeptides, and 50 tetrapeptides).The results of QSARs were superior to that of the earlier studies, with correlation coefficient (r(2)) and cross-validated(q(2)) equal to 0.902, 0.86; 0.985, 0.951 and 0.872, 0.77, respectively. By analysis, hydrophobic and steric properties of ACE-inh... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=5038913 Mon, 04 Jul 2011 23:00:00 +0100 5038913 http://www.medworm.com/index.php?rid=4995129&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21707519%26dopt%3DAbstract This article describes a novel method for predicting ligand-binding sites of proteins. This method uses only 8 structural properties as input vector to train 9 random forest classifiers which are combined to predict binding residues. These predicted binding residues are then clustered into some predicted ligand-binding sites. According to our measurement criterion, this method achieved a success rate of 0.914 in the bound state dataset and 0.800 in the unbound state dataset, which are better than three other methods: Q-SiteFinder, SCREEN and Morita's method. It indicates that the proposed method here is successful for predicting ligand-binding sites. PMID: 21707519 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4995129 Sun, 26 Jun 2011 23:00:00 +0100 4995129 http://www.medworm.com/index.php?rid=4995128&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21707520%26dopt%3DAbstract In this study we began with a statistical analysis of known inteins, which showed an unequal distribution of the three nucleophilic residues at positions 1 and +1, and then subjected six different mini-inteins to site-directed mutagenesis to systematically test the functionality of the three nucleophilic residues at the two positions. At position 1, most natural inteins had Cys and none had Thr. When the Cys at position 1 of the six inteins was mutated to Ser and Thr, the splicing activity was abolished in all except one case. At position +1, Cys and Ser were nearly equally abundant in natural inteins, and they were found to be functionally interchangeable in the six inteins of this study. When the two positions were studied as 1/+1 combination, the Cys/Ser combination was abundant in natu... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4995128 Sun, 26 Jun 2011 23:00:00 +0100 4995128 http://www.medworm.com/index.php?rid=4995127&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21707521%26dopt%3DAbstract Authors: Yamamoto H, Ben S, Saitoh S, Kamata K, Iguchi K, Hoshino M Galanin is a neuropeptide that is widely distributed in the central and peripheral nervous systems. In a previous study, we showed that a small cell lung carcinoma (SCLC) cell line, SBC-3A, released progalanin but not galanin, and that progalanin was then converted to galanin(1-20), the active form. Because the galanin(1-20) had undergone hydrolysis at Arg and Lys residues, the protease concerned was surmised to have a trypsin-like activity. The present study was performed to identify the trypsin-like protease which had previously been found to activate progalanin in this tumor tissue. The protease was isolated using chromatography and electrophoresis, and identified in tumor extracts from SBC-3A tumor-bearing mice; th... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4995127 Sun, 26 Jun 2011 23:00:00 +0100 4995127 http://www.medworm.com/index.php?rid=4995121&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21707522%26dopt%3DAbstract Authors: Singh P, Singh MK, Chauhan V, Gupta P, Dhaked RK Protein aggregation during expression, purification, storage, or transfer into requisite assay buffers hampers the use of proteins for in vitro studies. The formation of these aggregates represents a major obstacle in the study of biological activity and also restricts the spectrum of protein products being available for the biomedical applications. The catalytic light chain of botulinum neurotoxin type A undergoes autocatalysis and aggregation after purification upon long storage and freeze-thawing. In present study the conditions for the high level expression and purification of biologically active light chain protein of botulinum neurotoxin were optimized from a synthetic gene. Several cosolvents were screened in order to pre... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4995121 Sun, 26 Jun 2011 23:00:00 +0100 4995121 http://www.medworm.com/index.php?rid=4995120&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21707523%26dopt%3DAbstract Authors: Kabir SR, Hossen MA, Abu Zubair M, Alom MJ, Islam MF, Hossain MA, Kimura Y A lectin (designated as KRL) was purified from the extracts of Kaempferia rotunda Linn. tuberous rhizome by glucose-sepharose affinity chromatography. KRL was determined to be a 29.0±1.0 kDa polypeptide by SDS-PAGE under both reducing and non-reducing conditions. KRL was a divalent ion dependent glycoprotein with 4% neutral sugar which agglutinated different groups of human blood cells. Methyl-α-D-mannopyranoside, D-mannose and methyl-α-D-glucopyranoside were the most potent inhibitors. N-terminal sequence of KRL showed similarity to some mannose/glucose specific lectins but the main differences with their molecular masses and sugar content. KRL lost its activity markedly in the presence of denaturan... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4995120 Sun, 26 Jun 2011 23:00:00 +0100 4995120 http://www.medworm.com/index.php?rid=4995116&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21707524%26dopt%3DAbstract Authors: Fagundes FH, Aparício R, Dos Santos ML, Diz Filho EB, Oliveira SC, Toyama DO, Toyama MH A new secretory phospholipase A2 (sPLA2) isoform from Bothrops jararacussu venom (BjVIII) has been characterized by causing platelet aggregation, an absent activity in BthTx-I, Prtx-I and PrTx-II sPLA2s. According to our results, BjVIII also enhances insulin release by the pancreatic beta cells. The complete amino acid sequence of the new isoform was determined by Edman degradation and de novo peptide sequencing. These analyses showed a G35K amino acid modification for BjVIII in comparison with BthTx-I, PrTx-I and Prtx-II, a structural difference that has been related to the conflicting biological activities among BjVIII and other Lys49 sPLA2s. The whole set of evidences collected in this ... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4995116 Sun, 26 Jun 2011 23:00:00 +0100 4995116 http://www.medworm.com/index.php?rid=4995115&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21707525%26dopt%3DAbstract Authors: Cruces-Ángeles ME, Cabrera N, Pérez-Montfort R, Reyes-López CA, Hernández-Arana A Several variants of Saccharomyces cerevisiae triosephosphate isomerase (yTIM) were studied to determine how mutations of conserved and non-conserved Cys residues affect the enzyme. Wild-type yTIM has two buried free cysteines: Cys 41 (non-conserved) and the invariant Cys 126. Single-site mutants, containing substitutions of these cysteines with Ala, Val, or Ser (the three most conservative changes for a buried Cys, according to substitution matrices), were examined for stability and enzymatic activity. Neither of the Cys residues was found to be essential for enzyme catalysis. Determination of the global stability of the mutants indicated that, regardless of which Cys was substituted, individ... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4995115 Sun, 26 Jun 2011 23:00:00 +0100 4995115 http://www.medworm.com/index.php?rid=4946058&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21675945%26dopt%3DAbstract In conclusion, this pioneering study describes that the chitin-binding protein Mo-CBP(4), from M. oleifera seeds, exhibits anti-inflammatory and antinociceptive properties and scientifically supports the use of this multipurpose tree in folk medicine. PMID: 21675945 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4946058 Tue, 14 Jun 2011 23:00:00 +0100 4946058 http://www.medworm.com/index.php?rid=4946057&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21675946%26dopt%3DAbstract In this study, we constructed scFv that corresponded to the FV fragment of CR57, a monoclonal antibody against rabies virus, and called it FV57. Despite its virus neutralization activity, FV57 may or may not recognize the same epitope as that recognized by CR57. To resolve this issue, the binding epitope of rabies virus G protein recognized by FV57 was identified. A recombinant rabies virus G protein fragment (RVG179; residues 179-281) comprising several epitopes was expressed in E.coli, purified, and the specificity of its binding with FV57 was determined. In addition, a peptide (abbreviated as EP, residues 224-236) comprising the known epitope of G protein to which CR57 binds was synthesized and the potency of its binding with FV57 was also determined. The results showed that FV57 could ... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4946057 Tue, 14 Jun 2011 23:00:00 +0100 4946057 http://www.medworm.com/index.php?rid=4946056&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21675947%26dopt%3DAbstract Authors: Assreuy AM, Pinto NV, Mota MR, Meireles AV, Cajazeiras JB, Nobre CB, Soares PM, Cavada BS The vasorelaxant effect of the lectin of Pisum arvense (PAL) seeds was investigated in rat aorta. PAL (10-100 µg/ml) was applied on aorta rings, with or without endothelium, pre-contracted with phenylephrine (Phe; 0.1 µM). Participation of endothelium derived relaxant factors was evaluated incubating the tissue with indomethacin (10 µM), L-nitro arginine methyl ester (L-NAME, 100 µM) and tetraethylammonium (TEA, 5 mM) before addition of PAL. The role of the lectin domain was investigated by addition of PAL into tissue in presence of glucose (3x10(-5) M), or N-acetyl D-glucosamine (GlcNAc; 3x10(-4) M). The importance of extracellular calcium (Ca(2+)(e)) or interaction with muscarinic r... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4946056 Tue, 14 Jun 2011 23:00:00 +0100 4946056 http://www.medworm.com/index.php?rid=4946055&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21675948%26dopt%3DAbstract Authors: Safina D, Rafieva L, Demidyuk I, Gasanov E, Chestukhina G, Kostrov S The metalloproteinase from Thermoactinomyces sp. 27a (Mpr) represents secretory thermolysin-like metalloproteinases of the M4 family. The Thermoactinomyces enzyme is synthesized as a precursor consisting of a signal peptide, N-terminal propeptide, mature region, and C-terminal propeptide. The functional molecule lacks the signal peptide, N-terminal propeptide, and C-terminal propeptide, which indicates the processing of these regions. Until now, it remained unclear if the N-terminal propeptide is involved in the formation and functioning of Mpr, and the role of the C-terminal propeptide was also unclear. In this work, a Bacillus subtilis AJ73 strain expressing Mpr without the C-terminal propeptide-encoding re... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4946055 Tue, 14 Jun 2011 23:00:00 +0100 4946055 http://www.medworm.com/index.php?rid=4946054&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21675949%26dopt%3DAbstract Authors: Vasantha B, Vishwanatha TM, Sureshbabu VV Synthesis of N(α)-protected amino acyl azides starting from corresponding acids via the carbonyldiimidazole (CDI) activation is described. The protocol is extended for a one-pot preparation of ureido peptides that circumvents the isolation of acyl azide and isocyanate intermediates. The reaction was accomplished without using any additives and base. The protocol is simple, clean, high yielding and free from racemization. PMID: 21675949 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4946054 Tue, 14 Jun 2011 23:00:00 +0100 4946054 http://www.medworm.com/index.php?rid=4946053&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21675950%26dopt%3DAbstract In this study, we investigated whether the biological activity of endostatin 27 peptides can be enhanced by the addition of an integrin targeting sequence. RGDRGD and GGGRGD sequence were added to the carboxyl terminus of endostatin 27 and 25 peptides, respectively. Modification of endostatin 27 peptides with the RGD motif showed specific and increased binding to endothelial cells and the increased binding is consistent with improved antiangiogenic property. RGD-modified endostatin 27 peptides was more effective than human endostatin and endostatin 27 peptides in inhibiting liver cancer growth in athymic mice. These finding indicates that addition of a vascular targeting sequence can enhance the biological activity of an antiangiogenic peptides molecule. PMID: 21675950 [PubMed - as sup... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4946053 Tue, 14 Jun 2011 23:00:00 +0100 4946053 http://www.medworm.com/index.php?rid=4946052&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21675951%26dopt%3DAbstract Authors: Lin MC, Shen YF, Li G (2S,4aR,8aS)-Cis,cis-, (2R,4aS,8aR)-cis,cis-, rac-cis,cis-, and rac-trans,cis-decahydro-2-naphthyl-N-n-butylcarbamates are synthesized from condensation of (2S,4aR,8aS)-cis,cis-, (2R,4aS,8aR)-cis,cis-, rac-cis,cis-, and rac-trans,cis-decahydro-2-naphthols, respectively, with n-butyl isocyanate in the presence of triethylamine in dichloromethane. Optically pure (2S,4aR,8aS)-(-)- and (2R,4aS,8aR)-(+)-cis,cis-decahydro-2-naphthols are resolved by the porcine pancreatic lipase-catalyzed acetylation of decahydro-2-naphthols with vinyl acetate in t-butyl methyl ether. Absolute configurations of (2S,4aR,8aS)-(-)- and (2R,4aS,8aR)-(+)- cis,cis-decahydro-2-naphthols are determined from the (19)F NMR spectra of their Mosher's ester derivatives. (2S,4aR,8aR)-Trans,c... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4946052 Tue, 14 Jun 2011 23:00:00 +0100 4946052 http://www.medworm.com/index.php?rid=4946051&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21675952%26dopt%3DAbstract Authors: Dayer MR, Moosavi-Movahedi AA, Dayer MS, Mousavy SJ Hemoglobin is a tetrameric protein with two alpha and two beta subunits binds oxygen in a cooperative manner. In dominant tetrameric form of fish hemoglobin carry more than 90 percent of oxygen from gill to tissues at 20°C. The tetrameric form of fish hemoglobin is changed to monomeric form at low oxygen pressure in order to increase its oxygen affinity. This is one of adaptive mechanisms used by different kinds of fish. The major aim of this paper is to study the molecular basis of shirbot hemoglobin adaptation mechanism to various environmental conditions. Using different methods such as ion exchange chromatography, UV-Vis, fluorescence and circular dichroism spectroscopy, we extracted the main tetrameric fraction of shirb... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4946051 Tue, 14 Jun 2011 23:00:00 +0100 4946051 http://www.medworm.com/index.php?rid=4897770&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21605057%26dopt%3DAbstract Authors: Legowska A, Debowski D, Lukajtis R, Sztabkowska E, Mizeria A, Brzozowski K, Wysocka M, Lesner A, Rolka K Human β-defensin 3 (DEFB103) is a recently identified small cysteine-rich cationic peptide expressed ubiquitously upon local microbial invasion. A number of accumulating evidences indicate that this peptide is involved in many biological processes, including microbicidal activities, chemoattraction, and immunomodulation. In this article, we describe a novel approach through which we performed the expression and purification of the recombinant DEFB103 peptide in Escherichia coli (E. coli) based on the pTWIN1 expression system. This approach does not introduce any extra residues to the peptide product, and also eliminates the requirement of removing the fusion tag by exogeno... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4897770 Mon, 23 May 2011 23:00:00 +0100 4897770 http://www.medworm.com/index.php?rid=4897736&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21605058%26dopt%3DAbstract In this study, the peptides were designed to compare the effect of multiple Leu or Val residues as the hydrophobic side of an α-helical model on their structure, function, and interaction with model membranes. The Leu-rich peptides displayed 4- to 16-fold stronger antimicrobial activity than Val-rich peptides, while Val-containing peptides showed no haemolysis and weak cytotoxicity. The peptides LR and VR showed an α-helical-rich structure under a membrane-mimicking environment. Different cell selectivity for Leu- or Val-containing peptides correlated with the targeted cell membranes. The Leu-rich peptide LR(W) and Val-rich peptide VR(W) interacted preferentially with negatively charged phospholipids over zwitterionic phospholipids. VR(W) displayed no interaction with zwitterionic phosph... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4897736 Mon, 23 May 2011 23:00:00 +0100 4897736 http://www.medworm.com/index.php?rid=4897724&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21605059%26dopt%3DAbstract Authors: Lee CS, Lin CH, Hsieh WL, Chiao SM We have investigated the dependence of peptide oligomerization on intermolecular interaction in terms of both energetic and structural effect by PFGNMR. Three peptides, NPY([20-36] ), Pro34-NPY([20-36]) and NPY([21-31]), which are related to human NPY, were synthesized as models in this work. In contrast to NPY( [20-36]), both Pro34-NPY([20-36]) and NPY([21-31]) were found with descendent affinity with TFE cluster and continuous dissociating with increased temperature. The observed results can be accounted by the entropic change with temperature and the varied hydrophobic interactions between species due to the differed structures of peptides from each other. The removal of helical secondary structure or residues from C-terminal region may in... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4897724 Mon, 23 May 2011 23:00:00 +0100 4897724 http://www.medworm.com/index.php?rid=4897721&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21605060%26dopt%3DAbstract This study has shown that the galanin-LI released from SCLC SBC-3A cells consisted of the high-molecular-mass peptide form, and was processed extracellularly to galanin(1-20). Furthermore, galanin was seen to induce pro-MMP-2 and pro-MMP-9 release from SBC-3A cells. PMID: 21605060 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4897721 Mon, 23 May 2011 23:00:00 +0100 4897721 http://www.medworm.com/index.php?rid=4851222&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21592073%26dopt%3DAbstract Protein Pept Lett. 2011 May 19; Authors: Zhou GP PMID: 21592073 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4851222 Wed, 18 May 2011 23:00:00 +0100 4851222 http://www.medworm.com/index.php?rid=4851221&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21592074%26dopt%3DAbstract This study threw lights on the possibility of predicting the K(m) in beta-glucosidases based on their amino-acid features. PMID: 21592074 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4851221 Wed, 18 May 2011 23:00:00 +0100 4851221 http://www.medworm.com/index.php?rid=4851220&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21592075%26dopt%3DAbstract Authors: Harihar B, Selvaraj S In the past decade, when compared to models describing the folding rates of two-state proteins, models describing the folding mechanism of three-state proteins remain quite limited due to the complexity present in the folding mechanism and lack in their experimental data. In the present work, rate-limiting long-range contacts were classified into various bins based on sequence separation distance between the contacting residues and the role of these bins were analyzed for their importance in a data set of 35 three-state proteins. Predicting the folding rates of these proteins have been carried out by relating experimental folding rates and long-range contacts obtained from various sequence separation bins. For comparison, using the present model, predicti... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4851220 Wed, 18 May 2011 23:00:00 +0100 4851220 http://www.medworm.com/index.php?rid=4851219&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21592076%26dopt%3DAbstract This study allows initial inferences about the structure of the protease and will allow the rational design of its derivatives for structure-function studies and also for further improvement of the enzyme. PMID: 21592076 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4851219 Wed, 18 May 2011 23:00:00 +0100 4851219 http://www.medworm.com/index.php?rid=4851218&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21592077%26dopt%3DAbstract In this study, it was found that SI could synthesise α-arbutin using hydroquinone and sucrose as substrates, via an intermolecular transglycosylation reaction. Five phenylalanine residues (F185, F186, F205, F297, and F321) in the catalytic pocket of SI were chosen for site-directed mutagenesis. Mutants F185I, F321I, and F321W, whose hydrolytic activities were enhanced after the mutation, could synthesise α-arbutin through intermolecular transglycosylation with a more than two-fold increase in the molar transfer ratio compared with wild type SI. The F297A mutant showed a strong ability to synthesise a novel α-arbutin derivative and a four-fold increase in its specific activity for intermolecular transglycosylation over the wild type. Our findings may lead to a new way to synthesise novel... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4851218 Wed, 18 May 2011 23:00:00 +0100 4851218 http://www.medworm.com/index.php?rid=4851217&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21592078%26dopt%3DAbstract Authors: Liu XY, Wang SQ, Xu WR, Tang LD, Wang RL, Chou KC PPAR (peroxisome proliferator-activated receptor) pan agonists play a critical role in treating metabolic diseases, especially the Type-2 diabetes mellitus (T2DM). GlaxoSmithKline's sodelglitazar (GW677954) is one of the potent PPAR pan agonists, which is currently being investigated in Phase II clinical trials for the treatment of T2DM and its complications. The present study was aimed at investigation into the effect of sodelglitazar at the binding pockets of PPARs. The Schrodinger Suite program (2009) was used for the molecular docking, while the GROMACS program used for the molecular dynamics (MD) simulations. The results thus obtained showed that sodelglitazar being docked well in the active site of PPARs. It was revealed ... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4851217 Wed, 18 May 2011 23:00:00 +0100 4851217 http://www.medworm.com/index.php?rid=4851216&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21592079%26dopt%3DAbstract Authors: Shameer K, Pugalenthi G, Kandaswamy KK, Sowdhamini R 3D domain swapping is a protein structural phenomenon that mediates the formation of the higher order oligomers in a variety of proteins with different structural and functional properties. 3D domain swapping is associated with a variety of biological functions ranging from oligomerization to pathological conformational diseases. 3D domain swapping is realised subsequent to structure determination where the protein is observed in the swapped conformation in the oligomeric state. This is a limiting step to understand this important structural phenomenon in a large scale from the growing sequence data. A new machine learning approach, 3dswap-pred, has been developed for the prediction of 3D domain swapping in protein structure... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4851216 Wed, 18 May 2011 23:00:00 +0100 4851216 http://www.medworm.com/index.php?rid=4851215&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21592080%26dopt%3DAbstract In this study, we compared the binding potency of PB2 cap binding domain with two small molecules, i.e., RO and PPT28, with that of PB2 with cap analog m7GTP. The calculated binding energies showed that RO and PPT28 had higher binding affinity with PB2. Further interaction analysis showed that the important parts for binding were the five- and six-member heterocyclic rings （the 6/5-member rings) of small molecules, as well as the hydrophobic parts of RO and PPT28 which had good interactions with the hydrophobic residues in the binding cavity. Thus, RO and PPT28 are two potential anti-influenza drugs targeted PB2, which may inhibit the growth of influenza virus by competitively binding with the cap structure binding domain of PB2. PMID: 21592080 [PubMed - as supplied by publisher] (So... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4851215 Wed, 18 May 2011 23:00:00 +0100 4851215 http://www.medworm.com/index.php?rid=4851214&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21592081%26dopt%3DAbstract In this study, based on the combination of incremental convex hull, traditional geometric algorithm, and solvent accessible surface of proteins, we developed a novel approach for predicting the protein-ligand binding sites. Using PDBbind database as a benchmark dataset and comparing the new approach with the existing methods such as POCKET, Q-SiteFinder, MOE-SiteFinder, and PASS, we found that the new method has the highest accuracy for the Top 2 and Top 3 predictions. Furthermore, our approach can not only successfully predict the protein-ligand binding sites but also provide more detailed information for the interactions between proteins and ligands. It is anticipated that the new method may become a useful tool for drug development, or at least play a complementary role to the other exi... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4851214 Wed, 18 May 2011 23:00:00 +0100 4851214 http://www.medworm.com/index.php?rid=4851213&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21592082%26dopt%3DAbstract Authors: Zhang CY, Mazumdar M, Zhu DW, Yin DC, Lin SX The nucleation zone has to be reached for any crystal to grow, and the search for crystallization conditions of new proteins is a trial and error process. Here a convenient screening strategy is studied in detail that varies the volume ratio of protein sample to the reservoir solution in the drop to initiate crystallization that is named "composition modification". It is applied after the first screen and has been studied with twelve proteins. Statistical analysis shows a significant improvement in screening using this strategy. The average improvement of "hits" at different temperatures is between 32 and 42%, for examples, 41.8% ± 14.0% and 35.7% ± 12.4% (± standard deviation) at 288 K and 300 K, respectively. Remarkably, some n... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4851213 Wed, 18 May 2011 23:00:00 +0100 4851213 http://www.medworm.com/index.php?rid=4851212&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21592083%26dopt%3DAbstract Authors: Kawai Y, Matsuoka M, Kikuchi T One of the goals of molecular bioinformatics is decoding amino acid sequences to extract information on the principles of protein folding. However, this is difficult to perform with standard bioinformatics techniques such as multiple sequence alignment and so on. Thus, we propose a technique based on inter-residue average distance statistics to make predictions regarding the protein folding mechanisms of amino acid sequences. Our method involves constructing a kind of predicted contact map called an Average Distance Map (ADM) based on average distance statistics to pinpoint regions of possible folding nuclei for proteins. Only information on the amino acid sequence of a given protein is required for the present method. In this article, we summari... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4851212 Wed, 18 May 2011 23:00:00 +0100 4851212 http://www.medworm.com/index.php?rid=4851211&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21592084%26dopt%3DAbstract Authors: Zhou GP Physiologic relaxation of vascular smooth muscle is induced by the cyclic guanosine monophosphate (cGMP)-dependent protein kinase Iα enzyme (cGKIα), which activates myosin phosphatase (MLCP). This activation process is thought to occur through the interaction involving both N- and C-terminal leucine zipper coiled-coil (LZCC) domains of the kinase enzyme (cGKIα) with the myosin binding subunit (MBS) of MLCP. In this review, I summarize how to define the LZCC domains in both N-terminal cGKIα(1-59) and C-terminal MBS proteins using predictive and experimental methods, how to make a rapid and accurate structure determination of a cGKIα(1-59) molecule using NMR's residual dipolar coupling (RDC) measurements, and how to indentify the existence of a weak protein interact... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4851211 Wed, 18 May 2011 23:00:00 +0100 4851211 http://www.medworm.com/index.php?rid=4798068&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21534928%26dopt%3DAbstract Authors: Yu J, Xiang L, Zhang W A specific treatment of recurrent structural motifs that represent the local bias information has been proven to be an important ingredient in de novo protein structure predication. Significant majority of methods for local structure are based on building blocks, which still suffer from its inherent discrete nature. Instead of using building blocks, this work presents a new protocol framework for local structural motifs prediction based on the direct locating along protein sequence and probabilistic sampling in a continuous (Φ, ψ) space. The protein sequence was first scanned by an algorithm of sliding window with variable length of 7 to 19 residues, to match local segments to one of 82 motifs patterns in the fragment library. Identified segments were ... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4798068 Sun, 08 May 2011 16:15:03 +0100 4798068 http://www.medworm.com/index.php?rid=4798074&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21529338%26dopt%3DAbstract In this study we developed a disulfide trapping method that may reveal AcrB conformational changes under the native condition in the cell membrane. Specifically, we created seven disulfide bond pairs in the periplasmic domain of AcrB, which can be used as probes to determine local conformational changes. We have developed a rigorous protocol to measure the extent of disulfide bond formation in membrane proteins under the native condition. The rigorousness of the method was verified through examining the extent of disulfide bond formation in Cys pairs separated by different distances. The blocking-reducing-labeling scheme combined with fluorescence labeling made the current method convenient, reliable, and quantitative. PMID: 21529338 [PubMed - as supplied by publisher] (Source: Protein... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4798074 Sun, 01 May 2011 23:00:00 +0100 4798074 http://www.medworm.com/index.php?rid=4798073&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21529339%26dopt%3DAbstract Authors: Amani N, Saberi MR, Chamani J Separate and simultaneous binding effects of paclitaxel (a drug with anti-tumor activity) and estradiol (used for treating multiple maladies) with human serum albumin (HSA) were investigated by fluorescence quenching, UV absorption, circular dichroism, zeta potential and molecular dynamic techniques. An extensive fluorescence quenching was observed during the reaction of drugs and HSA and was rationalized in terms of a static quenching mechanism. The molecular distances between the donor (HSA) and acceptors (paclitaxel or estradiol) in binary and ternary systems were estimated according to Förster's theory of dipole-dipole non-radiation energy transfer. The features of drug-induced structural disturbances of HSA have been studied in detail by syn... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4798073 Sun, 01 May 2011 23:00:00 +0100 4798073 http://www.medworm.com/index.php?rid=4798072&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21529340%26dopt%3DAbstract Authors: Seixas FA, da Silva MR, Murakami MT, Tosqui P, Colombo MF Catalase is an enzyme that occurs in almost all aerobic organisms. Its main metabolic function is to prevent oxidative damage to tissues induced by hydrogen peroxide which is a strong oxidizing agent. Catalase is very effective in performing this task, since it has the highest turnover rate among all the enzymes. The properties of catalase have been investigated extensively for many years; however, the role of the solvent molecules in the catalytic reaction of this enzyme has not yet been investigated. Therefore, the objective of this work was to investigate the contribution of the solvent molecules on the catalytic reaction of bovine liver catalase with its substrate H(2)O(2) by the osmotic stress method. As a probe fo... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4798072 Sun, 01 May 2011 23:00:00 +0100 4798072 http://www.medworm.com/index.php?rid=4798071&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21529341%26dopt%3DAbstract In this study, by using a new combination of sequence, structure and energy features, we propose an iterative semi-supervised algorithm, SemiHS, to incorporate unlabeled data to improve the accuracy of hot spots prediction when sufficient training data is un-available and to overcome the imbalanced data problem. We evaluate the predictive power of SemiHS on a labeled set of 265 alanine-mutated interface residues in 17 complexes and a large unlabeled set of 2465 interface residues with 10-fold cross validation, and get an AUC score of 0.85, with a sensitivity of 0.70 and a specificity of 0.87, which are better than those of the existing methods. Moreover, we validate the proposed method by an independent test and obtain encouraging results. PMID: 21529341 [PubMed - as supplied by publis... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4798071 Sun, 01 May 2011 23:00:00 +0100 4798071 http://www.medworm.com/index.php?rid=4798070&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21529342%26dopt%3DAbstract Authors: Wang J, Wang XY, Shu M, Wang YQ, Lin Y, Wang L, Cheng XM, Lin ZH MHC-epitope binding plays a key role in the cellular immune response. Accurate prediction of MHC-epitope binding affinity can greatly expedite epitope screening by reducing costs and experimental effort. In this paper, 13 T descriptors， which derived from 544 physicochemical properties of the natural amino acids, were used to characterize 4 MHC class I alleles epitope peptide sequences, the optimal QSAR models were constructed by using stepwise regression combines with multiple linear regression (STR-MLR). For HLA-A*0201, HLA-A*0203, HLA-A*0206 and HLA-A*1101 alleles, the leave one out cross validation values (Q(2)(train)) were 0.581, 0.553, 0.525 and 0.588, the correlation coefficients (R(2)(train)) of trainin... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4798070 Sun, 01 May 2011 23:00:00 +0100 4798070 http://www.medworm.com/index.php?rid=4798069&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21529343%26dopt%3DAbstract In this study, a new method was proposed by combining the global information of PINs and protein sequence information. Random forest (RF) algorithm was implemented to develop the prediction model, and a high accuracy of 91.88% was obtained. Furthermore, the RF model was tested using three independent datasets with good performances, suggesting that our method is a useful tool for identification of PPIs and investigation into PINs as well. PMID: 21529343 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4798069 Sun, 01 May 2011 23:00:00 +0100 4798069 http://www.medworm.com/index.php?rid=4745134&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21443488%26dopt%3DAbstract Authors: Balhorn R, Balhorn DM PMID: 21443488 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4745134 Sun, 27 Mar 2011 23:00:00 +0100 4745134 http://www.medworm.com/index.php?rid=4745133&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21443489%26dopt%3DAbstract Authors: Kasinsky HE, Eirin-Lopez JM, Ausió J Despite their relatively arginine-rich composition, protamines exhibit a high degree of structural variation. Indeed, the primary structure of these histone H1-related sperm nuclear basic proteins (SNBPs) is not random and is the depository of important phylogenetic information. This appears to be the result of their fast rate of evolution driven by positive selection. The way by which the protein variability participates in the transitions that lead to the final highly condensed chromatin organization of spermatozoa at the end of spermiogenesis is not clearly understood. In this paper we focus on the transient chromatin/nucleoplasm patterning that occurs in either a lamellar step or an inversion step during early and mid-spermiogenesis. T... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4745133 Sun, 27 Mar 2011 23:00:00 +0100 4745133 http://www.medworm.com/index.php?rid=4745132&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21443490%26dopt%3DAbstract Authors: Kaur GS, Choudhuri J, D'Souza S During spermiogenesis, the elongating rat spermatid chromatin undergoes a gradual process of condensation which is initiated in the round spermatids at "step 7" of cytodifferentation in stage VII and extending to elongated spermatids at "step 19" of cytodifferentiation in stage VIII. The mechanism of chromatin condensation in the elongating spermatids is an elaborate process that encompasses several biochemical and biological aspects culminating in the deposition of protamine in DNA grooves. The protamination of sperm chromatin involves expression and storage of proteins involved in condensation, removal and degradation of nuclear histones and their replacement by transition proteins and protamine 1, transcriptional silencing and DNA repair, red... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4745132 Sun, 27 Mar 2011 23:00:00 +0100 4745132 http://www.medworm.com/index.php?rid=4745131&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21443491%26dopt%3DAbstract Authors: de Mateo S, Ramos L, de Boer P, Meistrich M, Oliva R Protamine 2 (P2) is synthesised as a precursor protein (pre-P2) which by proteolysis is processed to generate the mature components of the protamine 2 family of proteins (HP2, HP3 and HP4). In infertile patients, abnormal processing of the protamine 2 precursors has been suggested by the detection of an increased presence of precursor forms. However, the presence of small detectable amounts of precursor proteins has been demonstrated also in normal sperm samples, although the variation of pre-P2 in individual human sperm cells had not yet been explored. In the present manuscript we perform a mini-review describing what is known about protamine 2 precursors and P2 processing. In addition, we by immunofluorescence demonstrate ... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4745131 Sun, 27 Mar 2011 23:00:00 +0100 4745131 http://www.medworm.com/index.php?rid=4745130&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21443492%26dopt%3DAbstract Authors: Jones EL, Zalensky AO, Zalenskaya IA During late stages of spermatogenesis in mammals, most histones bound to DNA are replaced by protamines (PRM), which results in formation of supercondensed and genetically inert sperm chromatin. At fertilization, mature spermatozoon penetrates oocyte and chromatin is remodeled "back" from nucleoprotamine to nucleohistone state. While being crucial for activation of male genome and ultimately for initiation of embryonic development, this process is poorly studied, especially in humans. Data on model animals concerning PRM to histones exchange post fertilization are few and contradictory. As direct experimentation with human embryos is impossible due to ethical, legal and technical reasons, we evaluate the timing and mode of PRM removal in a ... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4745130 Sun, 27 Mar 2011 23:00:00 +0100 4745130 http://www.medworm.com/index.php?rid=4745129&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21443493%26dopt%3DAbstract Authors: Cree LH, Balhorn R, Brewer LR Single molecule studies of protamine-DNA interactions have characterized the kinetics of protamine binding to DNA and the morphology of the toroidal subunits that comprise sperm chromatin. The results provided by these studies are reviewed, the advantage of using single molecule techniques is discussed, and the implications of the results to the structure, kinetics of toroid formation, and stability of the DNA-protamine complex are described. New measurements of DNA condensation forces induced by the binding of protamine to DNA are also presented. These forces induce a significant tension in constrained segments of DNA and may contribute to the reduction in volume and shaping of the maturing spermatid cell nucleus. PMID: 21443493 [PubMed - as ... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4745129 Sun, 27 Mar 2011 23:00:00 +0100 4745129 http://www.medworm.com/index.php?rid=4745125&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21443494%26dopt%3DAbstract Authors: Nanassy L, Liu L, Griffin J, Carrell DT During spermiogenesis, human sperm undergo a dramatic reorganization of the chromatin in which canonical histones are replaced by two types of protamines, protamine 1 (P1) and protamine (P2). P1 and P2 are expressed approximately at a 1:1 ratio in healthy men. Alteration of this ratio is associated with male infertility. Patients with an abnormal P1/P2 ratio generally exhibit diminished semen quality, lower fertilization ability, and lower pregnancy rates when undergoing in vitro fertilization. Many studies have reported an elevated incidence of abnormal P1/P2 ratios in infertile men compared to fertile controls, and have evaluated the relationship between infertility and abnormal protamination; however, no prospective study has investig... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4745125 Sun, 27 Mar 2011 23:00:00 +0100 4745125 http://www.medworm.com/index.php?rid=4745124&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21443495%26dopt%3DAbstract Authors: Whit RJ, Plieger PG, Harding DR Two arginine side-chain protecting groups, N(G)-4-methoxy-2,3,6-trimethylbenzensulfonyl group (Mtr) and N(G)-2,2,5,7,8-pentamethylchroman-6-sulfonyl (Pmc), have been investigated at both the Arg(1) and/or Arg(9) position of the bioactive peptide, Bradykinin using Fluorenylmethyloxycarbonyl (Fmoc) Solid Phase Peptide Synthesis. A more efficient synthesis of the peptide has been found when a combination of Arg(Mtr) is present at position 1 and Arg(Pmc) is present at position 9 giving a cleaved pure yield of 52%. PMID: 21443495 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4745124 Sun, 27 Mar 2011 23:00:00 +0100 4745124 http://www.medworm.com/index.php?rid=4745123&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21443496%26dopt%3DAbstract Authors: Kar S, Drew MG, Pramanik A In the biomimetic design two hydrophobic pentapetides Boc-Ile-Aib-Leu-Phe-Ala-OMe (I) and Boc-Gly-Ile-Aib-Leu-Phe-OMe (II) (Aib: α-aminoisobutyric acid) containing one Aib each are found to undergo solvent assisted self-assembly in methanol/water to form vesicular structures, which can be disrupted by simple addition of acid. The nanovesicles are found to encapsulate dye molecules that can be released by the addition of acid as confirmed by fluorescence microscopy and UV studies. The influence of solvent polarity on the morphology of the materials generated from the peptides has been examined systematically, and shows that fibrillar structures are formed in less polar chloroform/petroleum ether mixture and vesicular structures are formed in more pol... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4745123 Sun, 27 Mar 2011 23:00:00 +0100 4745123 http://www.medworm.com/index.php?rid=4745122&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21443497%26dopt%3DAbstract Authors: Haque ME, Kawaguchiand K, Komatsu S Hypoxia caused by waterlogging results in a severe loss of crop production. At the primary stage of wheat development, the seminal roots have strategies to survive under hypoxia through alternative metabolism coupling root anatomical modification. The present study used a model system of lysigenous aerenchymatous seminal roots from a representative seedling stage of wheat to elucidate the root physiology in response to soil hypoxia. Seminal roots characteristic with lysigenous aerenchyma tissues were developed in pot cultures for 7 days under two hypoxic conditions, water depths of 15 cm below and 3 cm above the soil surface. Proteins from the roots were separated using two-dimensional polyacrylamide gel electrophoresis and identified using ... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4745122 Sun, 27 Mar 2011 23:00:00 +0100 4745122 http://www.medworm.com/index.php?rid=4745121&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21443498%26dopt%3DAbstract Authors: Zheng ZL, Guo L, Jia J, Xie CM, Zeng WC, Yang J One of the main challenges faced by biological applications is to predict protein subcellular localization in automatic fashion accurately. To achieve this in these applications, a wide variety of machine learning methods have been proposed in recent years. Most of them focus on finding the optimal classification scheme and less of them take the simplifying the complexity of biological systems into account. Traditionally, such bio-data are analyzed by first performing a feature selection before classification. Motivated by CS (Compressed Sensing) theory, we propose the methodology which performs compressed learning with a sparseness criterion such that feature selection and dimension reduction are merged into one analysis. The pr... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4745121 Sun, 27 Mar 2011 23:00:00 +0100 4745121 http://www.medworm.com/index.php?rid=4745120&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21443499%26dopt%3DAbstract Authors: An YJ, Lee JH, Jung HI, Sohn SG, Lee JJ, Park KS, Wu X, Jeong BC, Kang CM, Cha SS, Lee SH CTX-M-15, an extended-spectrum β-lactamase emerging worldwide, hydrolyzes lactam ring of β-lactam antibiotics, and thus causes therapeutic failure and a lack of eradication of pathogenic bacteria by third-generation β-lactams. Therefore, the enzyme is a potential target for developing agents against pathogens isolated from patients suffering from nosocomial infections. The CTX-M-15 protein was purified and crystallized at 298 K. X-ray diffraction data from CTX-M-15 crystal have been collected to 1.46 Å resolution using synchrotron radiation. The crystal of CTX-M-15 belongs to space group P2(1)2(1)2(1), with unit-cell parameters a = 45.50, b = 44.23, and c = 116.92 Å. Analysis of the ... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4745120 Sun, 27 Mar 2011 23:00:00 +0100 4745120 http://www.medworm.com/index.php?rid=4745119&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21443500%26dopt%3DAbstract Authors: Shimegi T, Takusagawa Y, Ohtsuki T, Noda S, Kurisu G, Kusunoki M, Ui S The development of a stable L-BDH chimera was attempted by exchanging whole domains between two native structural analogs, L-BDH and meso-BDH, because the S-configuration specificity of L-BDH is valuable from the standpoint of its application but its activity is unstable, whereas meso-BDH is stable. The domain chimeras obtained indicated that the leaf-like structures constituting three domains were likely to be mainly associated with chiral recognition, and the fourth domain, the basic domain, is likely to be mainly associated with enzyme stability. A combination of the leaf domains of L-BDH and the basic domain of meso-BDH attained a sufficient level of practical use as an artificial L-BDH chimera, because... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4745119 Sun, 27 Mar 2011 23:00:00 +0100 4745119 http://www.medworm.com/index.php?rid=4745118&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21443501%26dopt%3DAbstract Authors: Bretes E, Guranowski A, Nuc K This is report of mutational analysis of higher plant 5'-methylthioadenosine nucleosidase (MTAN). We identified and characterized the gene encoding yellow lupine (Lupinus luteus) MTAN (LlMTAN). The role of active site amino acids residues Glu24, Phe134, Glu188 and Asp211 was analyzed by site-directed mutagenesis. The Glu24Gln and Asp211Asn substitutions completely abolished the enzyme activity. The Glu188Gln mutant showed only trace activity toward 5'-methylthioadenosine. These results indicate that these three amino acid residues are necessary for enzyme activity. Furthermore, as the result of replacement of Phe134 by less bulky leucine, LlMTAN acquired the ability to bind and hydrolyze S-adenosylhomocysteine. We also analyzed the sequence of the... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4745118 Sun, 27 Mar 2011 23:00:00 +0100 4745118 http://www.medworm.com/index.php?rid=4745117&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21443502%26dopt%3DAbstract Authors: Zia-Ur-Rehman , Khan A G-protein coupled receptor (GPCR) is a protein family that is found only in the Eukaryotes. They are used for the interfacing of cell to the outside world and are involved in many physiological processes. Their role in drug development is evident. Hence, the prediction of GPCRs is very much demanding. Because of the unavailability of 3D structures of most of the GPCRs; the computational prediction of GPCRs is very demanding. In the present research, we have classified GPCRs into family, sub family and sub-sub family. We have extracted features using the hybrid combination of Pseudo amino acid, Fast Fourier Transform and Split amino acid techniques. The overall feature vector is then reduced using Principle component analysis. Mostly, GPCRs are composed o... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4745117 Sun, 27 Mar 2011 23:00:00 +0100 4745117 http://www.medworm.com/index.php?rid=4745116&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21443503%26dopt%3DAbstract In this study, we provide a simple approach to produce multiple epitopes within one recombinant protein in order to avoid the costly expression of less-effective pools of multiple proteins, which is the conventional strategy of diagnostic antigen production for HCV antibody detection. PMID: 21443503 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4745116 Sun, 27 Mar 2011 23:00:00 +0100 4745116 http://www.medworm.com/index.php?rid=4633699&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21413915%26dopt%3DAbstract Authors: Lalithamba HS, Hemantha HP, Sureshbabu VV The O-acyl isopeptide method has recently gained attention as an efficient protocol for the synthesis of 'difficult sequence' peptides. Herein, synthesis of three oligopeptides of different length, a pentapeptide Gly-Leu-Leu-Ser-Val, a heptapeptide fragment 285-291 of transmembrane (M7-24-T40) Ala-Val-Leu-Ser-Leu-Pro-Leu and a decapeptide, Gly-Leu-Leu-Ser-Val-Leu-Gly-Ser-Val-Ala were demonstrated in solution phase by employing O-acyl isopeptide method. The peptides were established through an efficient pH triggered intramolecular O→N acyl migration under physiological conditions. The reactions were clean and complete in appreciable length of time. PMID: 21413915 [PubMed - as supplied by publisher] (Source: Protein and Peptide Let... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4633699 Thu, 17 Mar 2011 00:00:00 +0100 4633699 http://www.medworm.com/index.php?rid=4633698&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21413916%26dopt%3DAbstract Authors: Gao CF, Qiu ZX, Wu XJ, Tian FW, Zhang H, Chen W Signal peptides recognition by bioinformatics approaches is particularly important for the efficient secretion and production of specific proteins. We concentrate on developing an integrated fuzzy Fisher clustering (IFFC) and designing a novel classifier based on IFFC for predicting secretory proteins. IFFC provides a powerful optimal discriminant vector calculated by fuzzy intra-cluster scatter matrix and fuzzy inter-cluster scatter matrix. Because the training samples and test samples are processed together in IFFC, it is convenient for users to employ their own specific samples of high reliability as training data if necessary. The cross-validation results on some existing datasets indicate that the fuzzy Fisher classifier is ... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4633698 Thu, 17 Mar 2011 00:00:00 +0100 4633698 http://www.medworm.com/index.php?rid=4633695&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21413917%26dopt%3DAbstract This study provides a novel method for directly analyzing cyclotide sequences without enzymatic digestion and further information regarding the distribution of cyclotides in plant species. PMID: 21413917 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4633695 Thu, 17 Mar 2011 00:00:00 +0100 4633695 http://www.medworm.com/index.php?rid=4633692&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21413918%26dopt%3DAbstract Authors: Ren Y, Chen X, Feng M, Wang Q, Zhou P On the basis of Bayesian probabilistic inference, Gaussian process (GP) is a powerful machine learning method for nonlinear classification and regression, but has only very limited applications in the new areas of computational vaccinology and immunoinformatics. In the current work, we present a paradigmatic study of using GP regression technique to quantitatively model and predict the binding affinities of over 7000 immunodominant peptide epitopes to six types of human major histocompatibility complex (MHC) proteins. In this procedure, the sequence patterns of diverse peptides are characterized quantitatively and the resulting variables are then correlated with the experimentally measured affinities between different MHC and their peptide... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4633692 Thu, 17 Mar 2011 00:00:00 +0100 4633692 http://www.medworm.com/index.php?rid=4633691&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21413919%26dopt%3DAbstract Authors: Rao S, Xu Z, Su Y, Li J, Sun J, Yang Y Recombinant antihypertensive peptide multimer (AHPM-2, 8kDa/68AA), a new designed polypeptide with potential antihypertensive effect in vivo, is composed of 15 low-molecular-weight antihypertensive peptides tandemly linked up according to the restriction sites of gastrointestinal proteases. After gene optimization, the DNA fragment encoding AHPM-2 was chemically synthesized, cloned into the pET32a, and successfully expressed in E.coli, above 90% in a soluble form. After chromatographic purification, the expressed fusion protein Trx-AHPM-2 was subject to the simulated gastrointestinal digestion, and the hydrolysate showed potent ACE inhibitory activity with an IC50 value of 4.5±0.3 μg ml-1. The active fragments from the AHPM-2 were ident... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4633691 Thu, 17 Mar 2011 00:00:00 +0100 4633691 http://www.medworm.com/index.php?rid=4633690&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21413920%26dopt%3DAbstract In this study, a different mode of pseudo amino acid composition (PseAAC) was proposed to formulate the protein samples by integrating the amino acid composition, the physic chemical features, as well as the composition transition and distribution features, where each of the protein samples was represented by a numerical vector through the sequence-based approach. Using the support vector machine algorithm, an accurate and reliable classifier was constructed to predict the thermophilic and mesophilic proteins. Moreover, three feature reduction algorithms were obtained for locating the most vital features and reducing the size of feature space. Among the three feature reduction algorithms, the genetic algorithm performed best. Finally, with the reduced features extracted from the genetic al... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4633690 Thu, 17 Mar 2011 00:00:00 +0100 4633690 http://www.medworm.com/index.php?rid=4633689&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21413921%26dopt%3DAbstract Authors: Kumar V, Saxena N, Sarma M, Kishan KV Hydantoinases are industrial enzymes with varying degree of activities on variable substrates to form different products. Although, few of the hydantoinase structures were known recently, the functional details and active site mechanism were not clearly understood yet. In a structure determination effort we reported that Bacillus sp. AR9 hydantoinase contains uncarboxylated lysine in the active site, whereas all the other hydantoinases have a carboxylated active site lysine. Here we describe the importance of carboxylated lysine for differential activities by making lysine mutations as well as carboxylating the lysine in a D-hydantoinase from Bacillus sp. AR9. The lysine to alanine and lysine to arginine mutations showed reduced activities... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4633689 Thu, 17 Mar 2011 00:00:00 +0100 4633689 http://www.medworm.com/index.php?rid=4633685&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21413922%26dopt%3DAbstract In this study, we constructed chimeric proteins containing ApoB-100 and/or hHSP60 peptides by human intestinal trefoil factor (ITF) as a scaffold and then fused with glutathionine-S transferase (GST) for expression in Escherichia coli. These purified chimeric proteins were used for immunizing apolipoprotein E (ApoE)-null mice fed on Western diet, and then the immune response and anti-atherosclerotic effect was assayed. Unexpectedly, neither anti-ApoB-100 nor anti-hHSP60 antibodies could be detected in serum. Histological analysis demonstrated the mice immunized with a chimeric protein containing both ApoB-100 and hHSP60 peptides showed the most significant reduction of atherosclerotic lesions (65.9%), and the mice immunized with the chimeric protein only containing ApoB-100 or hHSP60 pepti... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4633685 Thu, 17 Mar 2011 00:00:00 +0100 4633685 http://www.medworm.com/index.php?rid=4633684&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21413923%26dopt%3DAbstract Authors: Liu D, Chen Z Glutamine (GLN), which is the most abundant free amino acid of the human body, is an important cellular fuel and an essential precursor for the antioxidant glutathione (GSH). GLN plays a regulatory role in several cell specific processes, such as metabolism, protein synthesis and degradation, and respiratory burst. Severe GLN deficiencies usually occur rapidly in critical illness. GLN has regulatory capacity in immune and cell modulation, and GLN reduces morbidity and mortality in critical illness. The expression of heat shock proteins (HSP) is vital to cellular and tissue protection in stress or injury. GLN can function as a metabolic fuel and stress-signaling molecule in illness and injury via HSP. GLN has the ability to enhance HSP expression in injury, regula... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4633684 Thu, 17 Mar 2011 00:00:00 +0100 4633684 http://www.medworm.com/index.php?rid=4517493&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21342091%26dopt%3DAbstract Authors: Shi L, Xia Y, Zhang M, Yin SJ, Si YX, Qian GY, Lü ZR, Zhou HM, Zou F, Park YD Superoxide dismutase (SOD, EC 1.15.1.1) plays an important antioxidant defense role in organisms exposed to oxygen. Copper- and zinc-containing SOD (Cu/Zn-SOD) catalysis and the change in folding behavior of this enzyme in response to inactivators are therefore of interest. We studied the inhibitory effects of trifluoroethanol (TFE) on the activity and conformation of a Cu/Zn-SOD from Bos taurus. We found that TFE inactivated the enzyme and disrupted the tertiary and secondary structures of Cu/Zn-SOD. Kinetic studies showed that TFE-induced inactivation of Cu/Zn-SOD follows first-order reaction kinetics and that TFE binding sites are distinct from the copper- and zinc-containing active site. These s... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4517493 Mon, 21 Feb 2011 00:00:00 +0100 4517493 http://www.medworm.com/index.php?rid=4517492&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21342092%26dopt%3DAbstract Authors: Branco AT, Dos Santos Ferreira B, Lourenço GF, Lopes Marques VC, Tavares Machado OL, Pereira MG, Aquino Almeida JC, de Souza Filho GA β-1,3-glucanases are found in organisms as diverse as plants, animals, bacteria and fungi. In plants, such enzymes are not only associated with defense mechanisms against pathogens, but also play critical roles in physiological and developmental processes. Here we identified a new β-1,3-glucanase in maize seeds, and named it ZmGlucA. Sequence analysis revealed that ZmGlucA belongs to the class A of β-1,3-glucanase, a class related to defense and physiological processes in plants. mRNA and protein assays showed that zmGlucA is expressed exclusively in seeds, and it is differentially regulated during seed development. Additionally, zmGlucA exp... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4517492 Mon, 21 Feb 2011 00:00:00 +0100 4517492 http://www.medworm.com/index.php?rid=4517491&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21342093%26dopt%3DAbstract In this report, a novel strategy was designed to produce a soluble recombinant human LIF (rhLIF) in the prokaryotic system in order to obtain higher yields of the bioactive protein with simpler steps. This optimal hLIF gene was cloned, and it successfully expressed the soluble recombinant protein in E. coli using the thioredoxin (Trx) protein as a fusion partner. A simple purification procedure is established to purify the recombinant fusion protein from the soluble supernatant of the lysed culture cells. This procedure yields up to 5 mg/L rhLIF with above 95? purity. The strategy allows the protease to release target cytokines without additional N-terminus amino acids, which is an important consideration for maintaining its bioactivity. Functional analysis of the purified rhLIF by murine ... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4517491 Mon, 21 Feb 2011 00:00:00 +0100 4517491 http://www.medworm.com/index.php?rid=4517490&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21342094%26dopt%3DAbstract Authors: Tsuji-Ueno S, Komatsu M, Iguchi K, Takahashi M, Yoshino S, Suzuki M, Nemoto N, Nishigaki K Recent studies have been supporting that the generation of Aβ42 oligomers is responsible for Alzheimer's disease. Therefore, those peptides which bind to Aβ42 are scientifically interesting and can be possible candidates for the diagnosis and therapy of Alzheimer's disease. A systemic in vitro evolution, developed recently and the designated progressive library method (PLM), was applied to obtain Ab42-binding aptamers peptides. As a result, high affinity peptide aptamers made of 8 or 9 amino acids could be identified by this approach, endorsing the methodological effectiveness. Namely, the selection products from the secondary library of diversified peptides, which was constructed base... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4517490 Mon, 21 Feb 2011 00:00:00 +0100 4517490 http://www.medworm.com/index.php?rid=4517489&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21342095%26dopt%3DAbstract In this study, the distributions of N (N=2, 3) neighboring amino acids and the non-adjacent di-residue coupling patterns in the sequences of 65 thermostable and 77 thermophilic lipases had been systematically analyzed. It was found that the hydrophobic residues Leu, Pro, Met, Phe, Trp, as well as the polar residue Tyr had higher occurrence in thermophilic lipases than thermostable ones. The occurrence frequencies of KC EE KE RE, VE, YI, EK, VK, EV, YV, EY, KY, VY and YY in thermophilic proteins were significantly higher, while the occurrence frequencies of QC, QH, QN, HQ, MQ, NQ, QQ, TQ, QS and QT were significantly lower. CXP or CPX showed significantly positive to lipase thermostability, while XXQ or QXX showed significantly negative to lipase thermostability. Non-adjacent di-residue cou... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4517489 Mon, 21 Feb 2011 00:00:00 +0100 4517489 http://www.medworm.com/index.php?rid=4517488&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21342096%26dopt%3DAbstract Authors: Seneweera S, Kailasapathy K We investigated the delivery of calcium-alginate encapsulated peptidase (Flavourzyme(®), Aspergillus oryzae) on proteolysis of Cheddar cheese. Physical and chemical characteristics such as moisture, pH and fat content were measured, and no differences were found between control and experimental cheese at day 0. SDS-PAGE analysis clearly showed that proteolysis of α and k casein was significantly accelerated after three months of maturity in the experimental cheese. A large number of low molecular weight peptides were found in the water soluble fraction of the experimental cheeses and some of these peptides were new. N-terminal amino acid sequence analysis identified these as P(1), Leu-Thu-Glu; P(3), Asp-Val-Pro-Ser-Glu) and relatively abundant sta... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4517488 Mon, 21 Feb 2011 00:00:00 +0100 4517488 http://www.medworm.com/index.php?rid=4517487&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21342097%26dopt%3DAbstract Authors: Cui W, Josyula R, Li J, Fu Z, Sh B The protein translocations across mitochondrial membranes are carried out by specialized complexes, the Translocase of Outer Membrane (TOM) and Translocase of Inner Membrane (TIM). TIM23 translocon is responsible for translocating the mitochondrial matrix proteins across the mitochondrial inner membrane. Tim44 is an essential, peripheral membrane protein in TIM23 complex. Tim44 is tightly associated with the inner mitochondrial membrane on the matrix side. The Tim44 C-Terminal Domain (CTD) functions as an Inner Mitochondrial Membrane (IMM) anchor that recruits the Presequence protein Associated Motor (PAM) to the TIM23 channel. Using X-ray crystallographic and biochemical data, we show that the N-terminal helices A1 and A2 of Tim44 - CTD are ... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4517487 Mon, 21 Feb 2011 00:00:00 +0100 4517487 http://www.medworm.com/index.php?rid=4517486&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21342098%26dopt%3DAbstract Authors: Rákosi K, Szolomájer-Csikós O, Kalmár L, Szurmai Z, Kerékgyártó J, Tóth GK Mono-, di- and trisaccharide representing the reducing terminal of the core structure of N-glycans were incorporated into Leu-Lys-Asn-Gly-Gly-Pro hexapeptide that is a partial structure of the Trp-cage mini-protein by linear assembly. These studies provide evidence that the used combination of Fmoc and Boc strategy and mild conditions result in glycopeptides in high purity and reasonable yield. PMID: 21342098 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4517486 Mon, 21 Feb 2011 00:00:00 +0100 4517486 http://www.medworm.com/index.php?rid=4517485&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21342099%26dopt%3DAbstract Authors: Guruprasad L, Tanneeru K, Guruprasad K The virulent form of malaria is caused by Plasmodium falciparum that infects red blood cells. In order to survive inside the host, the parasite remodels the infected erythrocytes by exporting more than 300 effector proteins outside the parasitophorous vacuole membrane into the cytosol. The main feature of all the export proteins is the presence of a pentapeptide sequence motif; RxLxE/Q/D. This sequence motif is hydrolysed between L - x and the proteins with the acetylated new N-terminus xE/Q/D are exported. The enzyme responsible for this hydrolysis is plasmepsin V which is one of the ten aspartic proteases in P. falciparum. In order to understand the structural rationale for the specificity of this protease towards cleavage of the above ... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4517485 Mon, 21 Feb 2011 00:00:00 +0100 4517485 http://www.medworm.com/index.php?rid=4460308&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21265732%26dopt%3DAbstract Authors: Ramos C PMID: 21265732 [PubMed - in process] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4460308 Fri, 11 Feb 2011 05:30:03 +0100 4460308 http://www.medworm.com/index.php?rid=4460307&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21271976%26dopt%3DAbstract Authors: Arnórsdóttir J, Magnúsdóttir M, Friŏjónsson OH, Kristjánsson MM Aqualysin I, is a subtilisin-like serine proteinase, from the thermophilic bacterium Thermus aquaticus. It is predicted that the enzyme contains a salt bridge, D17-R259, connecting the N- and C-terminal regions of the enzyme. Previously we reported on the stabilizing effect of the incorporation of a salt bridge at a corresponding site in VPR, a related cold adapted enzyme from a marine Vibrio sp. Here we describe the effect of the reverse change, i.e. the elimination of the salt bridge on the thermal stability and kinetic properties of aqualysin I. Deletion of the putative salt bridge in the D17N mutant of the enzyme destabilized the enzyme by 8-9 °C in terms of T(50%), determined by thermal inactivation a... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4460307 Thu, 27 Jan 2011 00:00:00 +0100 4460307 http://www.medworm.com/index.php?rid=4460306&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21271977%26dopt%3DAbstract Authors: Carmo-Silva AE, Marri L, Sparla F, Salvucci ME Two Calvin Cycle enzymes, NAD(P)-dependent glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoribulokinase (PRK) form a multiprotein complex with CP12, a small intrinsically-unstructured protein. Under oxidizing conditions, association with CP12 confers redox-sensitivity to the otherwise redox-insensitive A isoform of GAPDH (GapA) and provides an additional level of down-regulation to the redox-regulated PRK. To determine if CP12-mediated regulation is specific for GAPDH and PRK in vivo, a high molecular weight complex containing CP12 was isolated from tobacco chloroplasts and leaves and its protein composition was characterized. Gel electrophoresis and immunoblot analyses after separation of stromal proteins by size frac... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4460306 Thu, 27 Jan 2011 00:00:00 +0100 4460306 http://www.medworm.com/index.php?rid=4460305&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21271978%26dopt%3DAbstract Authors: Hu L, Zheng L, Wang Z, Li B, Liu L Proteases are essential to most biological processes though they themselves remain intact during the processes. In this research, a computational approach was developed for predicting the families of proteases based on their sequences. According to the concept of pseudo amino acid composition, in order to catch the essential patterns for the sequences of proteases, the sample of a protein was formulated by a series of its biological features. There were a total of 132 biological features, which were sourced from various biochemical and physicochemical properties of the constituent amino acids. The importance of these features to the prediction is rated by Maximum Relevance Minimum Redundancy algorithm and then the Incremental Feature Selectio... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4460305 Thu, 27 Jan 2011 00:00:00 +0100 4460305 http://www.medworm.com/index.php?rid=4460304&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21271979%26dopt%3DAbstract Authors: Li YX, Shao YH, Deng NY Protein S-nitrosylation plays a key and specific role in many cellular processes. Detecting possible S-nitrosylated substrates and their corresponding exact sites is crucial for studying the mechanisms of these biological processes. Comparing with the expensive and time-consuming biochemical experiments, the computational methods are attracting considerable attention due to their convenience and fast speed. Although some computational models have been developed to predict S-nitrosylation sites, their accuracy is still low. In this work,we incorporate support vector machine to predict protein S-nitrosylation sites. After a careful evaluation of six encoding schemes, we propose a new efficient predictor, CPR-SNO, using the coupling patterns based encoding... Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4460304 Thu, 27 Jan 2011 00:00:00 +0100 4460304 http://www.medworm.com/index.php?rid=4460310&cid=s_37254_60_f&fid=37254&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21261583%26dopt%3DAbstract Protein Pept Lett. 2011 Jan 25; Authors: Dunn BM PMID: 21261583 [PubMed - as supplied by publisher] (Source: Protein and Peptide Letters) Protein and Peptide Letters journals http://www.medworm.com/rss/comments.php?id=4460310 Tue, 25 Jan 2011 00:00:00 +0100 4460310